An assessment of residence times of land-sourced contaminants in the Great Barrier Reef lagoon and the implications for management and reef recovery

Marine Pollution Bulletin 65 (2012) 267–279

Contents lists available at SciVerse ScienceDirect

Marine Pollution Bulletin

journal homepage: www.elsevier .com/locate /marpolbul

An assessment of residence times of land-sourced contaminants in the GreatBarrier Reef lagoon and the implications for management and reef recovery

Jon Brodie a,⇑, Eric Wolanski a,b, Stephen Lewis a, Zoe Bainbridge a

a Catchment to Reef Research Group, Australian Centre for Tropical Freshwater Research, James Cook University, Townsville, Queensland 4811, Australiab Australian Institute of Marine Science, PMB No. 3, Townsville, Queensland 43810, Australia

a r t i c l e i n f o

Keywords:WatershedRiver catchmentsSedimentNutrientPesticidesTrappingFlushingReef degradationReef recoveryClimate change

0025-326X/$ - see front matter � 2011 Elsevier Ltd. Adoi:10.1016/j.marpolbul.2011.12.011

⇑ Corresponding author. Tel.: +61 7 4781 6435; faxE-mail address: [email protected] (J. Brodie).

a b s t r a c t

We argue that the residence times of key pollutants exported to the Great Barrier Reef (GBR) are greaterin the GBR lagoon than those of the water itself, in contradiction to some previous assumptions. Adverseeffects of the pollutant discharge will be greater and longer lasting than previously considered, in turnrequiring stronger or more urgent action to remediate land practices. Residence times of fine sediments,nitrogen and phosphorus, pesticides and trace metals are suggested to be from years to decades in theGBR lagoon and highly likely to be greater than the residence time of water, estimated at around 15–365 days. The recovery of corals and seagrass in the central region of the GBR following current land-use remediation in the catchment depends on the residence time of these contaminants. Ecohydrologicalmodeling suggests that this recovery may take decades even with adequate levels of improved land man-agement practices.

� 2011 Elsevier Ltd. All rights reserved.

1. Introduction

The development of the Great Barrier Reef (GBR) catchmentsince European settlement (ca. 1830) has led to large increases inthe discharge of pollutants to the GBR; the sediment yield has risenby an estimated factor of 5.5, while total nitrogen and phosphorusloads have increased by factors of about 6 and 9, respectively(Kroon et al., 2012). Studies in the Fitzroy River, for example, haveshown that suspended sediment export has increased by a factor ofthree since European settlement. Additionally 50% of the modernfine sediment delivered by the Fitzroy River has been shown tobe trapped in the river floodplain and estuary (Bostock et al.,2007). The finer sediments are exported at least 30 km offshoreand possibly as far as the GBR mid-shelf (Ryan et al., 2007; Smithet al., 2008; Radke et al., 2010). It is important to quantify correctlythe residence time of these pollutants in the GBR lagoon whenevaluating the impact of human activities in the adjoining catch-ments, as well as the effectiveness of remediation measures.

Concepts such as the residence time, flushing rates and the ageof water have been put forward to quantify the retention of waterin estuarine or coastal environs (Deleersnijder et al., 2001; Monsenet al., 2002; Oliveira and Baptista, 1997; Wolanski, 2007). The res-idence time is the amount of time that a parcel of water spends inan estuary or in coastal waters before it is transported to the openocean. The flushing time is the time for the concentration of a

ll rights reserved.

: +61 7 4781 5589.

tracer to fall to within 1/e (0.37) of its original value. The age isthe time of water to transit the estuary from the river to the ocean.

The residence time is a widely used metric to understand andpredict the effects of contaminants in estuarine and coastal waters(Jickells, 1998). The value of the residence time of pollutants suchas fine sediment, nutrients, trace metals and pesticides is differentfrom that of water because these materials may not be simply car-ried passively by water currents, a process called conservativetransport, but they may also be affected by processes such as floc-culation, sorption biological uptake and settling and/or resuspen-sion, all processes of non-conservative transportation (Wolanski,2007).

There have been a number of previous studies of residencetimes or flushing times of water in the GBR lagoon. Hancocket al. (2006) used radium isotopes as tracers to estimate that theinner lagoon flushing time of water was 18 days in the southernGBR and 45 days in the central GBR. Luick et al. (2007) used hydro-dynamic models with simulated neutrally buoyant tracer particlesto estimate that residence times can vary from ca. 1 month–1 year.Wang et al. (2007) used salinity as a tracer to estimate flushingtimes to be around 40 days for water close to the coast and 14 daysfor water in the offshore reef matrix. Most recently, Choukrounet al. (2010) used satellite-tracked drifters to estimate that theGBR residence time of water is in the order of a few weeks for mostof the GBR lagoon.

There is no justification to assume that river pollutant or soluteresidence times are equal to water residence times. Indeed, as dis-cussed by Alongi and McKinnon (2005), Furnas et al. (2005, 2011)and Luick et al. (2007), the circulation of coastal waters is sluggish,

268 J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279

giving enough time for bio-available nutrients and organic matterto be taken up by biota and recycled several times before being ex-ported to the surrounding seas by oceanic currents.

The bulk of land-derived pollutants are delivered by riverfloods; if they were carried by the water in a conservative manner,they would be swiftly flushed out of the GBR and have negligibleimpact on the GBR. Much of the rivers’ freshwater discharge occursin short-lived flow events, with on average 2–3 floods per year forsmall rivers in the wetter areas and 1 flood per year for the largerdry tropical rivers (Furnas, 2003). River flood times typically rangefrom a few days for a small river draining a catchment <1000 km2

(e.g. see the example of the Ross River in Lambrechts et al., 2010) toa few weeks and up to a few months for the GBR’s two largestrivers, the Burdekin (�130,000 km2) and Fitzroy (�140,000 km2)River catchments (King et al., 2001; Webster and Ford, 2010;Bainbridge et al., 2012).

While oceanographic models are available to estimate the resi-dence time of water in the GBR (e.g. Luick et al. 2007), there cur-rently lacks an adequate sediment transport and biogeochemicalmodel to directly estimate residence times of the major pollutantsdelivered by rivers to the GBR lagoon. Given this lack of knowledgethe only possible path to estimate residence times of pollutants isto review existing data and known processes occurring in shelfwaters that affect these pollutants. In many papers there is animplication that water residence times are either closely linkedto pollutant residence times (Wang et al., 2007) or that water res-idence times will provide strong evidence to assess pollutant resi-dence times (Hancock et al., 2007; Choukroun et al., 2010). It isthen implied that as water residence times are short (tens to hun-dreds of days) solute and pollutant residence times are equallyshort and these substances may thus not present a great hazardto GBR ecosystems. This assumption is based on an implied beliefthat the pollutants of interest (suspended sediment – SS, nutrientsand pesticides) behave in a conservative manner during mixing inthe GBR lagoon and hence ‘‘follow the water’’. In fact it is very wellknown that SS and nutrients do not behave in a conservative man-ner (Devlin and Brodie, 2005; Devlin and Schaffelke, 2009; Devlinet al., 2001; Wolanski, 2007; Brodie et al., 2010; Bainbridge et al.,2012). Pesticides may initially mix in a conservative manner (Lewiset al., 2009a) but in the longer term degradation removes themfrom the water column.

In this synthesis of existing data and process understanding, wehave two purposes. The first purpose is to clarify the difference be-tween the residence (or the flushing) time of water (and conserva-tively mixed solutes) and that of non-conservative materials,including sediments, nutrients, metals and pesticides, which arethe major contaminants to the GBR. We argue that the residencetimes of these key terrestrial pollutants are significantly greaterin the GBR lagoon than those of the water itself, in contradictionto some previous assumptions.

The second purpose is to use the concept of residence times toassess the likely effectiveness of land-based remediation measuresfor the health of the GBR. This analysis was done by quantifying thetransport time scales of the hydrodynamic processes resulting inthe transport and fate of pollutants in coastal and estuarine watersof the GBR. Analysis of these values provides an estimate of theresulting time scales for recovery of the GBR from remediationmeasures in the adjoining catchments. Our approach focuses onquantifying the processes that result in different predicted trajec-tories for GBR coral cover during this century.

2. Physical attributes of the GBR shelf

The GBR lies adjacent to the Queensland coast, primarily on thecontinental shelf between 9 �S and 24 �S. The width of the shelf

varies from 50 km in the north to 200 km in the south and canbe arbitrarily divided into an inner shelf immediately adjacent tothe coast, with depths to 20 m, a middle shelf with depths of 20–40 m and an outer shelf with depths of 40–100 m. The inner shelfis significantly influenced by catchment and coastal processes withsediments dominated (greater than 80%) by granitic-derived fluvialdetritus (terrestrial material) i.e. silicoclastic and aluminosilicateclay and silt (Belperio, 1983; Maxwell, 1968). The middle shelf issediment starved while the sediments on the outer shelf are dom-inated by biogenic carbonate material (Mathews et al., 2007).

Oceanographic field and numerical studies reveal that the pre-vailing water circulation is controlled by the wind, the tides andthe circulation in the Coral Sea driven by the South Equatorial Cur-rent (SEC) which flows towards the GBR (Black, 1993; James et al.,2002; Kingsford and Wolanski, 2008; Lambrechts et al., 2008;Luick et al., 2007; Wolanski, 1994). The SEC can intrude on the con-tinental shelf in the north-central region of the GBR; it bifurcates,generating a net northward current (the North Queensland Cur-rent, NQC) to the north of the bifurcation point and a southwardcurrent (the East Australian Current, EAC) to the south of the bifur-cation point (Brinkman et al., 2002). This circulation is furthermodified by the wind; for small to moderate winds the net circu-lation is modified mainly only in shallow inshore waters; strongwinds may prevent the SEC intruding on the GBR continental shelf,and in that case the NQC and EAC may remain offshore from theGBR continental shelf (Choukroun et al., 2010). This implies thatthere is a swift flushing of GBR waters during windy periods, withtypical flushing times of 10–30 days. Under such conditions thereis also a long-distance connectivity of different parts of the reefat scales of up to hundreds of kilometres along the shelf.

In reef waters, this swift flushing effect is greatly reduced be-cause of bathymetric steering which results in the trapping ofwaters in a coastal boundary layer around individual reefs as wellas in a reef matrix (i.e. the ‘sticky water’ effect; Spagnol et al.,2001). This results in patchiness in the distribution of passivelydrifting waterborne larvae, so that some larvae remain trapped inhigh retention zones while others can be advected over large dis-tances. There is evidence for this oceanographic prediction in thegenetic study of van Oppen et al. (2008), which focused on larvaldispersal and population connectivity of Seriatopora hystrix, abrooding coral, and shows that the majority of the larval recruitsare locally drawn while a minority (�4%) are drawn from a migra-tion at relatively large spatial scales (tens–hundreds of kilometres).

A sharp delineation exists in estuarine behaviour between thewet season (December–April) and the dry season. During the dryseason, little or no freshwater discharge occurs and the estuary be-haves as a tidal inlet with a typical water flushing time of 7 days forsmall estuaries (Wolanski and Ridd, 1990; Andutta et al., 2011) andup to one month for the largest, the Fitzroy River estuary (Websterand Ford, 2010). Reprocessing of materials occurs during this sea-son such as wind-driven movement of sediments up the coast andsubsequent trapping in mangroves and northward-facing bays(Larcombe et al., 1995; Larcombe and Woolfe, 1999; Orpin et al.,2004; Woolfe and Larcombe, 1999) as well as seaward export innepheloid layers (Brinkman et al., 2004).

During the wet season, the estuaries are commonly fresh at theriver mouth and the mixing zone is located in coastal waters, i.e.within river plumes (Dagg et al., 2004). River plumes commonlyfirst spread longshore northward from the river mouth for dis-tances of tens of km to 200 km and later spread seaward (Fig. 1;Wolanski and Jones, 1981; Wolanski and van Senden, 1982; Devlinand Brodie, 2005; Brodie et al., 2010; Bainbridge et al., 2012;Devlin et al., 2012; Schroeder et al., 2012). Most suspended solidsand particulate nutrients are deposited within a few kilometres ofthe river mouth (Devlin and Brodie, 2005; Bainbridge et al., 2012).In the Burdekin plume, suspended solid concentrations decrease

Fig. 1. Progression (a–c) of a multiple river plume in the Wet Tropics (9, 11, 13 February 2007, respectively) extending from the coast to beyond the outer reef. The lines showthe outer edge of the plume made visible due to Coloured Dissolved Organic Matter and phytoplankton. Images (a–c) show the transformation from a plume dominated byterrestrial particulate matter into a plume dominated by a dissolved nutrient driven phytoplankton bloom. A proportion of the contained nutrients in the plume may be seen‘escaping’ to the Coral Sea in part c. Image courtesy of CSIRO. From Brodie et al., 2011.

J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279 269

from �500 mg 1�1 in the river at nominally zero salinity to<10 mg l�1 at salinity of 10 psu (Fig. 2). While the duration of riverplumes in the GBR seldom last more than a month (King et al.,2001), plumes can reach most reefs of the GBR; indeed, satelliteimages taken in February 2007, after a period of heavy rains, foundcatchment discharges traveling as far as 130 km offshore to theouter areas of the GBR (Fig. 1). Similarly in the central GBR, plumesfrom the Pioneer and O’Connell Rivers were observed more than100 km from the coast (Brodie et al., 2010) and plumes are regu-larly detected throughout the GBR at these distances (Schroederet al., 2012). In 2011, plumes from the Mary, Burnett, Fitzroy andBurdekin and Wet Tropics Rivers filled the GBR inner shelf out toabout 50 km from the coast from Fraser Island in the south to CapeTribulation in the north, a distance of approximately 1200 km(Brodie et al., 2012; Bainbridge et al., 2012).

Terrestrial material is found in benthic sediments in a bandalong the coast on the inner shelf (Lambeck and Woolfe, 2000).Further offshore, on the mid and outer shelf, less terrestrial derivedmaterial is found in benthic sediments. This pattern has been com-monly observed in studies on the composition of benthic sedimentand biota. In transects across the GBR shelf terrestrial biomarkerchemicals such as pentacyclic triterpenoid alcohols and long-chainnormal alkanes (Currie and Johns, 1989; Johns et al., 1994; Shawand Johns, 1985; Shaw and Johns, 1986), land-sourced trace metals(Brady et al., 1994), d13C in corals and sediments (Gagan et al.,1987; Risk et al., 1994), d15N in corals (Sammarco et al., 1999)

and trace metals in coral skeletons (Alibert et al., 2003; Lewiset al., 2012; Wyndham et al., 2004) change from a predominatelyterrestrially influenced signal inside 20 km to much lower influ-ence beyond 50 km. However there is evidence of fine sedimentmovement as a nepheloid layer from inshore to 30 km offshorenear Cairns (Brinkman et al., 2004; Wolanski and Spagnol, 2000a).

3. Fate of sediments

3.1. Coarse sediment

Studies have shown that considerable amounts of coarse sed-iments are transported in large Burdekin River floods as bed loadmaterial where up to 6 m of the river bed may become displacedand redeposited at one time (Fielding et al., 1999). While much ofthis sediment may become incorporated within overbank flood-plain deposits (e.g. Alexander et al., 1999), the sediment that isdelivered to the coast forms highly dynamic deltaic environmentswhich shape the present coastline and change over time with riv-er avulsion. Thirteen separate deltaic lobes have been identifiedfor the Burdekin River over the last 10,000 years (Fielding et al.,2006). In the case of the Fitzroy River, bedload sediment deliveredto Keppel Bay is advected northwards initially by strong tidaldynamics followed by shoreward movement due to the windeventually forming subaqueous dune complexes (Ryan et al.,

Fig. 2. Scatter plot of (�) suspended particulate matter (SPM) versus salinity in the Burdekin River plume on 21–22 February, 2002. The straight line indicates the expectedSPM if it displayed conservative mixing behaviour. Data from Brodie et al. (2004).

270 J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279

2007) and estuarine and floodplain (Bostock et al., 2007) andcoastal dune/beach ridge deposits (Brooke et al., 2008). Agedeterminations of the floodplain deposits suggest that they havebeen formed over the course of the last 8000 years (Bostocket al., 2007). The beach ridge data (Brooke et al., 2008) show thatthese ridges trap an estimated 79% of the total bedload sedimentsdelivered from the Fitzroy River. The ages of these ridgesshow they were deposited at rapid intervals at over the last1500 years.

The residence time of this coarse riverine sediment in the GBR isthus thousands of years as it is incorporated in beaches, sand spits,subaqueous dunes and Chenier deposits and are largely availableto be redistributed over relatively long periods (Fielding et al.,2006; Lacombe and Carter, 2004; Bostock et al., 2007; Ryan et al.,2007). For example, the extensive Bowling Green Bay sand spit(north of the Burdekin River) formed approximately 1000 yearsago (Fielding et al., 2006). The impact of changing coarse sedimentdelivery to the GBR is more likely to influence the geomorphologyof coastlines rather than impact directly on marine ecosystems ex-cept for species that are reliant on the coastal zone. Largeimpoundments such as the Burdekin Falls Dam retain nearly allcoarse sediments and thus reduce coarse sediment delivery tothe coast dramatically (Cooper et al., 2006; Faithful and Griffiths,2000; Lewis et al., 2009b). These large dams also reduce peak riverfloods and may increase sedimentation in the riverbed and estuar-ies downstream, similarly to the case of the Ord River, WesternAustralia (Wolanski et al., 2001, 2004a,b). Reduced transport ofcoarse sediments in the coastal zone due to reservoir construction,shipping channel dredging and other coastal development hasresulted in local-scale erosion of beaches within the GBR (e.g.Muller et al., 2006).

3.2. Fine sediment

There is evidence that the delivery of fine sediments have mark-edly increased since European settlement (c. 1830) in the adjoiningcatchment (Kroon et al., 2012; Neil et al., 2002). Fine sediment is asignificant polluter as it is exported in large quantities from clearedlands to rivers and estuaries, it increases turbidity and reduceslight penetration and photosynthesis, and it forms mud banks insheltered coastal waters (Lambrechts et al., 2010; Wolanski andSpagnol, 2000a).

Fine sediment does not travel with the water currents becauseit settles out in calm waters and is resuspended by currents andwaves. The residence times of water are thus irrelevant to the fateof fine sediment and its impact on the GBR. This is evidenced bythe transformation of the Cairns coast from a sandy beach in1888 into a muddy coast by 1999 (Duke and Wolanski, 2001).These field data suggest that the residence time of fine sedimentin the GBR is measured in decades and possibly centuries. In thecase of the Maroochy River, immediately to the south of the GBR,estimated sediment residence times in the estuary are up to30 years (Douglas et al., 2009).

Field and model studies of fine sediment transport (Margve-lashvili et al., 2006; Wolanski et al., 2005, 2008; Ryan et al.,2007; Lambrechts et al., 2010; Webster and Ford, 2010) and depo-sition (Orpin et al. 2004; Webster and Ford, 2010) for both smalland large rivers in the GBR show a number of sediment transportpathways. Firstly, the export of fine sediment is largest duringand immediately following a river flood. Secondly, a major portionof the load settles in coastal waters immediately following a riverflood. Thirdly, both seaward export and estuarine trapping of thefine sediment occurs after the flood has ceased and this can last

J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279 271

several months and in some cases years after a large river flood.Lastly, strong winds and currents resuspend the fine sedimenteven during low flow years. The final deposition areas are in shel-tered bays and leeward of headlands and islands in areas of lowwave activity and small tidal currents (Orpin et al., 2004; Wolanskiet al., 2008; Lambrechts et al., 2010).

Fine sediments are temporally supply-limited in GBR coastalwaters as they are related to resupply from flood events that, aspointed out earlier, are episodic (Larcombe and Woolfe 1999).However the key factor for coastal reefs is the residence time offine sediment in shallow reef and coastal waters. This is controlledby sediment winnowing by wind waves, a process which exportssediment from shallow reef waters to slightly deeper surroundingareas (Storlazzi and Jaffe, 2008) or to sheltered northward-facingbays (Orpin et al., 2004). Sediment may also be transported backinto the estuary by tidal currents (e.g. Bryce et al., 1998). Wind-dri-ven currents and waves generated by storms or cyclones are theprime agents for the redistribution of fine sediments on the innershelf of the GBR lagoon (Lambrechts et al., 2010; Larcombe andCarter, 2004; Wolanski et al., 2005, 2008). This process results inlower turbidity levels at the end of the dry season than at the startof the dry season for a given wind speed and tide.

While recent research has highlighted the importance of parti-cle size and organic content in the transport capacity of these finesediments within the GBR lagoon (Bainbridge et al., 2012) and theirenhanced effects on corals compared to inorganic sediment (We-ber et al., 2006), the fate of organic-rich fine sediments is stillpoorly understood (Wolanski et al., 2008). Organic-rich particlescan be destroyed through biological activity and thus may haveconsiderably shorter residence time than mineral particles. Finesediments remain ‘bioactive’ while they are able to have effectson the biota, for example, through resuspension leading to reducedlight to benthic biota or through sedimentation onto the benthicbiota.

From the above information we estimate the residence time offine sediments in the GBR lagoon to be not less than one year, as issuggested for water, but of the order of decades to centuries, thusclearly much greater than water residence times.

4. Fate of nutrients

Nutrients entering coastal waters are extensively modifiedwithin estuaries and estuarine plume zones. Plumes in the GBRare usually turbid, at least initially, as a result of the high sus-pended particulate matter (SPM) loads in rivers; hence, primaryproductivity is limited by light availability (Devlin and Brodie,2005; Turner et al., 1998). Water-column light levels improve asthe turbidity declines, whereby primary production becomes a ma-jor process in transforming bioavailable nutrients in the water col-umn (Dagg et al., 2004). Dissolved inorganic forms are mostimmediately available to phytoplankton. Dissolved and particulateorganic nutrients can be broken down in the water column by bac-teria and zooplankton, and in the sediments primarily by bacteria,which, in time, become available for plant growth (Furnas et al.,2011).

GBR shallow coastal waters are turbid during strong winds dueto wind-driven resuspension and in some regions strong tidal cur-rents. The fate of nutrients in turbid waters is controlled by the finesediment because much of the nutrients are adsorbed to the sedi-ment (Middelburg and Herman, 2007). During calm conditions thefine sediments settle on the bottom and the associated nutrientsare thus not available to primary productivity in the water column;these nutrients however are processed by benthic microbesresulting in reduced net burial of nutrients in subtidal sedimentsover the long term (Alongi and McKinnon, 2005; Furnas et al.,2011). During resuspension events these nutrients are mixed back

into the water column and are utilized by phytoplankton as shownby elevated chlorophyll concentrations (Walker, 1981).

A robust discussion is currently occurring globally as to thenecessity of reducing nitrogen (N) loads or phosphorus (P) loadsor both to prevent eutrophication in estuarine, coastal and marineenvironments (Conley et al., 2009; Howarth et al., 2011; Paerl,2009). Such considerations are also relevant to the GBR which isbelieved to be N limited in most circumstances (Furnas et al.,2005, 2011). The relative importance of N and/or P managementin the GBR catchment area for protecting ecosystem health in theGBR lagoon is still being debated.

4.1. Nitrogen

For this discussion we need to define the term ‘Reactive Nitrogen(RN)’, which we will use throughout the analysis as the N whose res-idence time and flushing rates we are interested in. Nitrogen com-pounds in nature can be divided into two groups: non-reactiveand reactive. The most important non-reactive form (except for fix-ation processes, see below) of N is dinitrogen (N2), the main constit-uent of the atmosphere. Reactive N includes all biologically active Ncompounds in the biosphere. Thus, reactive N includes inorganicforms of N such as ammonia (NH3), ammonium (NHþ4 ), nitrate(NO�3 ) and nitrite (NO�2 ) (together referred to as dissolved inorganicnitrogen – DIN), and some organic forms (e.g., urea, amines, proteins,and nucleic acids) which can be present in water as dissolved organicnitrogen (DON) or particulate nitrogen (PN). Many forms of DON areconsidered to have limited bioavailability and thus might not be in-cluded in the reactive N category although the actual proportion ofDON which is bioavailable varies between water bodies and is oftendifficult to determine (Seitzinger et al., 2005; Furnas et al., 2011). AllPN is considered to be potentially bioavailable as it is easily able to beconsumed by organisms such as filter feeders and then utilisedthrough the digestive system, while bacteria can grow on and con-sume some forms of particulate organic matter. In this discussionwe will also include all forms of N present in living biota (fish, phy-toplankton, bacteria, benthic algae, corals, etc.) as part of the reactiveN pool as this N is still within the biologically available pool. Theavailability of reactive N in marine ecosystems is affected by inputsof reactive N e.g. N2 fixation, atmospheric deposition, river dis-charge, ocean upwelling (Furnas et al., 1997, 2005), losses of reactiveN e.g. denitrification, burial in sediments and transport out of thesystem (to the Coral Sea) and stores of reactive N in the system (inthe sediment, water column, biota) (Furnas et al., 2011).

Reactive N enters the GBR lagoon in river discharge as DIN, DONand PN and as well from upwelling (mostly DIN) and throughatmospheric deposition (DIN) and N fixation (Bell et al., 1999; Fur-nas et al., 1997, 2005, 2011). The river discharge component, thesubject of the current analysis, is largely delivered during regularhigh flow river events (Devlin and Brodie, 2005). During floodplume dispersal, RN is transformed by physical, chemical and bio-logical processes such that much of the RN is retained in the GBRlagoon albeit in a different form to which it entered (e.g. Daviesand Eyre, 2005). Immediately bioavailable forms such as nitrateand ammonium are rapidly assimilated by phytoplankton (primar-ily) and to a lesser extent benthic plants (Furnas et al., 2005) oncelight conditions become favourable, usually at SS concentrations inthe plume water column of <10 mg L�1 (Dagg et al., 2004; Devlinand Brodie, 2005; Turner et al., 1990). Phytoplankton is then rap-idly and completely consumed by mesozooplankton (Alongi andMcKinnon, 2005; McKinnon and Thorrold, 1993; Furnas et al.,2005) and subsequently by macrozooplakton such as fish larvae(Thorrold and McKinnon, 1995). These forms of ‘large’ particulateorganic nitrogen are then able to be utilised by macro organismssuch as fish and reef invertebrates; thus, they pass into ‘long-term’(i.e. considerably longer than one year) storage in the system. Most

272 J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279

of the organic matter (and contained nutrients) produced on thereef is recycled and retained in living organisms or sediments with-in the reef system (Ayukai, 1995; O’Neil and Capone, 2008; Suzukiet al., 1995). Hence, much of the stocks of RN in the GBR are held inthe biota both on the reef and inter-reef as well as in the sedimentand the water column.

Nitrogen may also be trapped in the GBR lagoon as forms ofDON which are less bioavailable i.e. not part of the RN pool. Thelargest proportion (often more than 90%) of N in lagoon waters ispresent as DON (Furnas et al., 2005, 2011) and while some of thismaterial is a result of direct discharge of DON from rivers, most is aresult of autochthonous production in the lagoon. The actual bio-availability of DON is still open to discussion but generally it is con-sidered to be of limited bioavailability except for the small fractionof simpler organic compounds (Bronk et al., 2006) and the compo-nent discharged from rivers (Seitzinger and Sanders, 1997). Thelargest fraction within DON includes refractory compounds thatpersist for months to hundreds of years (Bronk, 2002) includinghumic and fulvic acids, porphorins, and amides. The highly bio-available fractions include urea, dissolved free amino acids and nu-cleic acids (Bronk, 2002) which turnover on timescales of minutesto days and can be directly utilized by a variety of organismsincluding animals such as echinoderm larvae (Hoegh-Guldberg,1994) as well as marine phytoplankton (Seitzinger et al., 2002).However, recent research has shown (Bronk et al., 2006) a smallfraction of the refractory pool may be bioavailable to some phyto-plankton. Hence, some of the DON load is also able to be trapped inthe biota before being flushed from the lagoon.

In contrast, a large portion (�90%) of the PN rapidly settles outof river plumes with suspended sediment close to the river mouth(Bainbridge et al., 2012; Devlin and Brodie, 2005). The PN is avail-able to bacteria, plankton and protists, thus being trapped in the la-goon in the biota and becoming part of the food chain (Dagg et al.,2004; Mayer et al., 1998). The PN can also be directly utilized bybenthic algae when in contact with algal fronds through bacterialmediation (Schaffelke, 1999). While remineralisation and turnoverrates for N in benthic sediments are relatively rapid in the GBR,considerable time is required for the overall cycle of remineralisa-tion and subsequent uptake by phytoplankton and benthic plants(Chongprasith, 1992; Ulman and Sandstrom, 1987).

Mechanisms for removal of RN from the GBR lagoon are denitri-fication, burial in sediments and flushing. Bacterial denitrificationas a mechanism of removal of RN is an important process through-out the coastal zone (Seitzinger, 1988). This process occurs primar-ily in sediments with a large organic matter content and lowoxygen status. Denitrification has high potential to remove RN inthe conditions of the GBR (Alongi and McKinnon, 2005; Furnaset al., 2005, 2011; but see Burgin and Hamilton, 2007). Burial ap-pears to be a lesser mechanism as frequent resuspension, burrow-ing animal activity and remineralisation prevent high rates ofburial (Alongi and McKinnon, 2005; Alongi et al., 2006; Brunskillet al., 2002; Furnas et al., 2011).

Studies in plumes (Devlin and Brodie, 2005; Devlin and Schaff-elke, 2009; Brodie et al., 2010, 2011) suggest that little RN escapesthe GBR lagoon during the period plumes are detectable – usually afew weeks following discharge. Some component of the RN may beflushed out of the lagoon into the Coral Sea as phytoplankton. Sa-tellite images using chlorophyll as a proxy for RN suggest that thisquantity is small (Fig. 1). Estimates of time scales of removal of RNare thus quite variable – both short (denitrification and part exportto Coral Sea) and long (burial, recycling through biota). Hence,residence time in the GBR is mostly determined by biota turnoverand eventual denitrification when present in a suitable form(Alongi and McKinnon, 2005; Furnas et al., 2011). Residence timesof RN will not be short as is the case with water but likely years todecades due to nutrients being ‘fixed’ in organisms such as fish,

coral and macroalgae, the lifetime of which is measured in yearsalthough N exchanges continuously occurs between the organismsand the environment. As a result of the increased N input from theland and the long residence time of N, the GBR lagoon is becomingenriched in N and this is reflected in elevated chlorophyll concen-trations in certain zones (Brodie et al., 2007, 2011; De’ath andFabricius, 2008, 2010).

Hence, there is little correlation of these residence times withthe residence times of water in the GBR lagoon. We argue thatthe residence time of nitrogen from runoff to the GBR is signifi-cantly greater than the water itself, in contradiction of some previ-ous assumptions (e.g. Wang et al., 2007). Overall, from the datapresented, it is unlikely that N residence times are less than oneyear, similar to water, but instead they are of the order of yearsto decades.

4.2. Phosphorus

Phosphorus is delivered to the GBR in a number of chemicalforms (Tappin, 2002). These include particulate phosphorus (PP)which can be a mixture of particulate inorganic phosphorus (PIP)and particulate organic phosphorus (POP). The POP is mainly detri-tal organic matter and is most likely to be bioavailable in the coastalenvironment through ingestion by filter feeders and bacterialgrowth on the particles. The PIP is mainly mineral P forms such asapatite, which is unlikely to be bioavailable, and also phosphate ad-sorbed onto sediment particles that is readily bioavailable afterdesorption in the marine environment (Froelich, 1988). Other formsof P are dissolved organic phosphorus (DOP) that comprise plantdetrital material but are probably less bioavailable than POP anddissolved inorganic phosphorus (DIP). The DIP is composed of phos-phate and polyphosphates which are readily bioavailable. As withN, the bioavailable (even in the long-term) fractions of P can beclassed as ‘reactive phosphorus’ (Tappin, 2002).

The retention of P in the coastal zone is often due to adsorption onparticulate matter, and trapping in estuarine and coastal shelf sedi-ments. Adsorption of P onto particulate matter containing iron andaluminum oxides is particularly effective (Krom and Berner, 1980).The behavior of P in estuarine systems is also influenced by thestrong physico-chemical gradients, which result from the variationsin pH, ionic strength and ion species composition between the fresh-water and seawater (Froelich, 1988; van der Zee et al., 2007). The re-moval of P can occur through bacterial reduction of phosphate togaseous phosphine. However, little is known on the rate of phos-phate–phosphine transformation and its contribution to overall Pcycling (Tappin, 2002). On the global scale, it is generally acceptedthat intertidal sediments are more efficient for P burial than for N(Howarth et al., 1995) and that P burial is mostly of less biologicallyavailable fractions (e.g. apatite) as the bioavailable fraction is recy-cled back into the water column (Sundby et al., 1992).

Monbet et al. (2007) found that P speciation varies greatly in aGBR inshore – offshore transect with organic P and authigenic(apatite) P the major chemical forms and that burial efficiency var-ies significantly over the shelf. Inshore areas showed significant Premobilization from sediments to the water column (up to�50%). The mid and the outer shelf showed little evidence forremobilization (except for coral reef platform sediments), withmore of the sediment P being in the less reactive authigenic apatitephases. An appreciable fraction of this non-labile authigenic apa-tite phase was identified as fish bone. In the sites adjacent to coralreefs, McCulloch et al. (2003a) showed that basalt-derived sedi-ments can account for >90% of the terrestrial P, although makingup less than half of the total terrigenous detritus. They also showedthat P enters the GBR lagoon via a two-stage process. Firstly, duringepisodic flood events, P is transported into the GBR lagoon fromrivers on fine suspended sediments, with heavy initial sedimenta-

J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279 273

tion of the PP near the river mouth and with only minor desorptionof P occurring in the low-salinity flood plumes (Brodie andMitchell, 1992; McCulloch et al., 2003a). Release of phosphate fromsediments after mineralization of PP (Furnas et al., 2011), occursmainly over longer timescales, predominantly in regions of sedi-ment anoxia, with diffusion directly into sediment pore watersduring calm weather and subsequent release into the water col-umn via sediment resuspension during windy periods. This processresults in P depletion of the sediments and low concentrations of Pin GBR inshore benthic sediments (McCulloch et al., 2003a).

Similarly to N, there is little correlation of these residence timeswith the residence times of water in the GBR lagoon and that theresidence time of phosphorus from runoff to the GBR is signifi-cantly greater than the water itself. Thus it is unlikely P residencetimes are less than one year, as for water residence times, but ofthe order of years to decades.

5. Fate of pesticides and trace metals

5.1. Pesticides

The presence of soluble herbicides in the GBR lagoon measured/accumulated in passive samplers at ng L�1 concentrations duringthe dry season (Kennedy et al., 2012; Shaw and Müller, 2005; Shawet al., 2010) suggest that the Reef Plan (2009) priority herbicides(atrazine, diuron, hexazinone, tebuthiuron and ametryn) for man-agement have relatively high persistence in the marine environ-ment. Concentrations of these herbicides are around 1–10% ofthe wet season concentrations, which may reflect their half lifein water (hydrolysis) of about 40–100 days, though possibly con-siderably longer as some herbicides (diuron and ametryn) are sta-ble from hydrolysis in water (‘Footprint’ Pesticide PropertiesDatabase: http://sitem.herts.ac.uk/aeru/footprint/en/index.htm).These herbicides inhibit photosynthesis at the photosystem II stage(PSII herbicides) and appear to be transported to the GBR lagoon inthe dissolved phase, although around one third of the diuron loadmay be transported in the particulate phase (Davis et al., 2012).This finding agrees with previous studies that have detected diuronresidues in the intertidal/subtidal sediments of the GBR lagoon(Haynes et al., 2000). Mixing and dispersion of these pesticides inthe GBR lagoon during flood plumes is essentially a conservativeprocess and thus the herbicides are dispersed well offshore (Lewiset al., 2009a) with only diuron likely to be trapped inshore throughparticle settling. Thus, diuron may be more persistent in the GBRthan the other PSII herbicides due to its ability to adsorb to partic-ulate matter. Other pesticides which have a stronger affinity toparticulate phases such as the banned organochlorine insecticides(e.g. DDT, dieldrin) continue to be detected in sediments and biotaof the GBR (Haynes et al., 2000; Negri et al., 2009) and have consid-erably longer residence times due to their much longer degrada-tion rates (30–50 year half lives).

Overall, it appears that the residence times of pesticides in theGBR lagoon are not governed by water flushing times but ratherby their decay rates and their associations with either the dissolvedor particulate phases. The relatively short soil half lives of the pri-ority PSII herbicides delivered to the GBR lagoon suggests that theirresidence time is probably in the order of 1–3 years.

5.2. Trace metals

High resolution analysis of coral cores provides insights into thebehaviour of certain soluble trace metals in the GBR lagoon. Forexample, elevated barium concentrations in coral skeletons gener-ally coincide with river discharge to the GBR lagoon and are linkedto desorption from clays in the low salinity mixing zone (McCul-

loch et al., 2003b; Sinclair and McCulloch, 2004). However, bariumalso displays ‘tail’ behaviour following certain floods where ele-vated concentrations continue well after the flood event and sea-water salinity has returned to normal; this suggests that anotheras yet unidentified source of barium is required to explain thisbehavior (Alibert et al., 2003). The residence time of ‘new’ bariuminputs to the GBR lagoon is relatively short (i.e. flushed once salin-ities return to normal) although the sources of ‘anomalous’ bariumindicate that it could be stored in the GBR before being re-releasedback into the water column (Sinclair, 2005; Lewis et al., 2012).Alternatively, some barium may be permanently stored in biotasuch as in coral skeletons or foraminifera.

Elevated manganese (Mn) concentrations in coral cores maycoincide with flood events as Mn in suspended sediments isphoto-chemically reduced to the soluble +2 form (Lewis et al.,2007). However, elevated coral Mn is also linked to the spring/summer months and related to either photoreductive dissolutionof suspended particulate Mn oxides or a diagenetic release of Mnat the seawater–sediment interface from reducing conditions in-duced by the decay of organic matter (Alibert et al., 2003; Wynd-ham et al., 2004). These findings suggest that ‘new’ Mn deliveredto the GBR most likely binds with iron-oxide minerals and thenis recycled back into the water column in the warmer spring andsummer months. Therefore, the residence time of Mn is relativelylong (i.e. until buried below the sediment resuspension zone ren-dering it inert or trapped in biota such as coral skeletons). Lewiset al. (2007) found considerably elevated Mn concentrations (orderof magnitude enrichment) in a Magnetic Island coral core between1850 and 1900 which coincided with European settlement and thestocking of sheep and cattle in the Burdekin River catchment. Itwas suggested that elevated Mn was linked to increased sedimenterosion of basaltic-rich soils. However, due to the lower samplingresolution of the coral (2-year intervals) it was not known if coralMn concentrations returned to baseline levels during the dry sea-son before another ‘pulse’ of Mn was delivered in the next wet sea-son. Malcolm McCulloch (pers. comm.) has re-analysed this coralcore at higher resolution which shows that Mn indeed remainedelevated in the coral throughout the year and over the entire50 year period. This finding implies that the delivery of ‘new’ mi-cro-nutrients to the GBR lagoon is of particular importance andsome trace metals such as Mn may have relatively long residencetimes in the system.

Concentrations of toxic trace (‘heavy’) metals detected insurface waters and in algae within the GBR lagoon in the 1980ssuggested an uncontaminated environment (Denton and Burdon-Jones, 1986a,b). Considerable levels of Fe, Zn, Cu, Cd and Ag havebeen found in the livers of dugongs from the GBR although thesource of these metals is thought to be natural (Denton et al.,1980). Elevated levels of heavy metals in benthic sediments andin marine life from the GBR lagoon have only been reported inareas surrounding the major ports and harbours in the region(Haynes and Johnson, 2000). Townsville hosts the main shippingport in the central GBR and benthic sediments near the port con-tain elevated levels of Cd, Cu, Pb and Zn (Gibbs, 1993; Reicheltand Jones, 1994; Doherty et al., 2000). Concentrations of Cu, Pband Zn in sediments surrounding the inshore coral reefs of Mag-netic Island increased significantly following channel dredgingfor the Townsville Port (Reichelt and Jones, 1994). Corals in closeproximity to the Townsville Port also contain elevated heavy metalconcentrations (Esslemont, 2000).

A large mercury (Hg) spike (500 ppb compared to 12 ppb back-ground) was discovered in a sediment core from Bowling GreenBay (Walker and Brunskill, 1996, 1997). Pb-210 dating places thisspike around the 1870–1890’s which coincides with the historicaluse of Hg to extract gold in the Charters Towers district (Walkerand Brunskill, 1996, 1997). In addition, Hg also increased towards

274 J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279

the top of a sediment core from Upstart Bay. This increase wasattributed to the use of organomercurial herbicides and fungicidesin the sugarcane industry (Walker and Brunskill, 1996, 1997).

In Port Curtis (Gladstone), a harbour serving heavy industry andmineral exports in the southern GBR, arsenic, nickel and chromiumconcentrations in sediments exceeded sediment quality guidelinesand some metals were also enriched in the biota but all water sam-ples were below guidelines (Jones et al., 2005). In a later study An-gel et al. (2010) found concentrations of metals (Cd, Hg, Cu, Zn, Ni.Mn, Fe, Al) inside Port Curtis to be generally elevated compared tooutside the harbour in GBR lagoon waters. Esslemont et al. (2004)has shown that at least some of these metals can become incorpo-rated into corals that grow in close proximity to ports.

Studies of heavy metals in coastal crabs (Australoplax tridentataand Scylla serrata) along the GBR coast show that elevated concen-trations of some metals can be found reflective of the concentrationsin the adjacent sediment and water with higher concentrations nearcentres of heavy industry, urban areas and ports compared to lessdeveloped locations (Mortimer, 2000; Negri et al., 2009).

The data suggest that the residence times in the GBR lagoon fortrace metals are highly variable and depend on the chemical prop-erties of each particular element. Many of the toxic trace metalsdischarged into GBR coastal waters from industrial activity appearto be trapped in coastal sediments and biota, also producing longterm enrichment of close coastal waters compared to the open,better flushed waters of the GBR lagoon. Based on the availabledata residence times of most metals are likely to be 10s of yearsin bioactive form but variable with individual metals which aregoverned by their oceanic residence times (see Taylor and McLen-non, 1985).

Fig. 3. Time-series plot of the predicted average live coral cover on 261 reefsbetween Bowen and Lizard Island (�500 km apart) in the recent past and in thefuture to 2100 for four scenarios of alternative developments of Australia and theWorld. For Australia: scenario 1 = business as usual with a focus on material well-being; scenario 2 = focus on social and environmental well-being resulting inhalving of the watershed export of fine sediment and nutrients. For the world:scenario A = business as usual with climate change not stabilized and reaching850 ppm CO2 by 2100; scenario B = focus on social and environmental well-beingresulting in climate change stabilized at 350 ppm CO2. Observational data are (+)from Bruno and Selig (2007) and (�) from Sweatman et al. (2011); the data mayunderestimate historical coral loss because nearshore reefs were not surveyed.Modified from Costanza et al. (2011).

6. Implications for the GBR and its coral reefs

6.1. Residence time and recovery

Deliveries of fine sediments, nutrients and pesticides havemarkedly increased since European settlement in the adjoiningcatchment a century ago (Neil et al., 2002; Brodie et al., 2012;Kroon et al., 2012). As detailed above the residence time of land-derived pollutants (fine sediment, reactive nitrogen and phospho-rus, PSII herbicides and trace metals) in the GBR is much longerthan that of water and as a result these pollutants have time to de-grade the ecosystems of the GBR. The impact is readily apparent ina number of indices pointing to the decreased health of the GBR;they include a 40% decrease from 1980–1983 to 2000–2003 ofthe average coral cover in the GBR (Bruno and Selig, 2007)although a smaller but still significant decrease is suggested bySweatman et al. (2011) for the period 1986–2004; decline in inter-tidal seagrass health along a large section of the central GBR coast(McKenzie et al., 2010); a 50% decrease from 1927–1928 to 1998 ofthe Secchi disk visibility at Low Isles in the central region of theGBR (Wolanski and Spagnol, 2000b); the transformation of theCairns coast from a sandy beach in 1888 into a muddy coast in1999 (Duke and Wolanski, 2001); and increasing eutrophicationof coastal waters (Brodie et al., 2011). Hughes et al. (2011) in par-ticular explained the link between water quality and coral coverdecline.

As the residence time of fine sediment and associated nutrientsin the GBR is measured in decades, the beneficial impact for deep(depth > �5 m) coastal coral reefs of improved land-use practicesmay not be seen for a corresponding period. However, because ofwinnowing of fine sediment by waves, some beneficial impactmay be evident within a year on wave-swept, shallow reefs. Thefull beneficial effect for GBR corals may not be felt for decades untilthe coastal, accretionary wedge of fine sediment derived from the

last 100 years of land-use is exported from, or is consolidated with-in, coastal waters. This situation was observed in Kaneohe Bay, Ha-waii. After the bulk nutrient input was removed from the Bay bydiverting the sewage effluent outfall to the ocean, coral reef recov-ery was delayed by several years until nutrients stored in the sed-iments were dispersed and natural reef ecology processes wererestored (Hunter and Evans, 1995; Kinsey, 1988; Smith et al.,1981; Stimson et al., 2001). A case study from Cleveland Bay hasshown that the number of clear water days over the corals growingin depths less than 3 m would be 200 per year if sediment runoffwas cut by half, as opposed to 60–90 days at present (Lambrechtset al., 2010).

Long residence times of land-derived contaminants, from yearsto decades, suggest a potential buildup within the GBR lagoon gi-ven that increased above natural delivery of these contaminantsoccurs on an annual basis. The implications of accumulation arethat threshold levels of contaminants may be reached and ecolog-ical damage occurs. The slow reduction of contaminant stockswithin the GBR also means that management resulting in de-creased contaminant inputs may take many years to result in reefrecovery.

6.2. Management of the GBR

The Australian and the Queensland governments recognized thethreats to the GBR from catchment based activities by launchingthe Reef Water Quality Protection Plan in 2003 (Reef Plan, 2003),which was revised and updated in 2009 (Reef Plan, 2009). Reef Planaims to (1) reduce the pollutant load from non-point sources in thewater entering the Reef; and (2) rehabilitate and conserve areas(e.g. wetlands) that have a role in removing water borne pollu-tants. It specifically targets nutrients, pesticides and sediment

Table 1Estimated residence times for materials discharged from Great Barrier Reef rivers within the lagoon.

Material dischargedfrom GBR rivers

Estimated residence time in the GBRlagoon

Published evidence to support this estimate

Freshwater 15–365 days Hancock et al. (2006), Luick et al. (2007), Wang et al. (2007) and Choukroun et al. (2010)

Coarse sediment 1000’s of years Larcombe and Carter (2004), Fielding et al. (2006), Bostock et al. (2007), Ryan et al. (2007), Brookeet al. (2008)

Fine sediment 10’s of years in bioactive form Lambeck and Woolfe (2000), Wolanski and Spagnol (2000a), Duke and Wolanski (2001), Larcombeand Carter (2004), Orpin et al. (2004), Ryan et al. (2007), Smith et al. (2008), Wolanski et al. (2008),Radke et al. (2010), Lambrechts et al. (2010) and Webster and Ford (2010)

Reactive Nitrogen Years - decades Ayukai (1995), Furnas et al. (1997), Furnas et al. (2005), Furnas et al. (2011), Suzuki et al. (1995),Bronk, (2002), Alongi and McKinnon (2005), Davies and Eyre (2005), Devlin and Brodie (2005), O’Neiland Capone (2008), Devlin and Schaffelke (2009), Brodie et al. (2010) and Brodie et al. (2011)

Reactive Phosphorus Years – decades Brodie and Mitchell (1992), Furnas et al. (1997), Furnas et al. (2005), Furnas et al. (2011), McCullochet al. (2003a), Davies and Eyre (2005) and Monbet et al. (2007)

PSII herbicides 1–3 years Haynes et al. (2000), Shaw and Müller (2005), Lewis et al. (2009)a, Shaw et al. (2010), Davis et al.(2012), Kennedy et al. (2012)

Trace metals 10s of years in bioactive form butvariable with individual metals

Alibert et al. (2003), McCulloch et al. (2003b), Sinclair and McCulloch (2004), Wyndham et al. (2004),Lewis et al. (2007); 2012; Walker and Brunskill (1996, 1997) and Mortimer (2000).

J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279 275

which wash into waterways or leach into groundwater, mainly as aresult of agricultural activities in reef catchments. The Reef Plantargets include a 20% reduction in suspended sediment dischargeby 2020 and 50% reductions in N, P and pesticide (PSII herbicides)discharge by 2013 (Reef Plan, 2009). In 2009 the updated ReefWater Quality Protection Plan was endorsed by the Queenslandand Australian Governments. The Federal Government has pro-vided $200 million under the Reef Rescue Initiative which providesfinancial incentives to farmers and landholders to improve theirland management practices that reduce the run-off of nutrients,pesticides and sediments from agricultural land. Considering thesize of the catchments and of the associated problems the currentlevel of management action may turn out to be inadequate or inef-fectual in practice (Kroon, 2012; Thorburn and Wilkinson, inpress).

More recently (2009) the Queensland Government introducedlegislation (the Reef Protection Amendment Act) requiring sugar-cane farmers and graziers in the Wet Tropics, Burdekin and MackayWhitsunday regions of the GBR catchment to, in some cases, sub-mit environmental risk management plans (ERMPs) to the Depart-ment of Environment and Resource Management for accreditationand in general to compulsorily adopt a suite of best managementpractices. This legislation is meeting much resistance, includingprotest rallies, by some landholders and the success of its imple-mentation is yet to be seen (Brodie et al., 2012).

Numerical models of coral cover may be a useful tool to quan-tify the human impact on GBR coral cover (Costanza et al., 2011;Richmond and Wolanski, 2011). They demonstrate (e.g. see thehindcast predictions in Fig. 3 up to the year 2010) that the com-bined impact of natural, acute disturbances and long-term, chronichuman impact during the last 100 years has degraded the GBR. Asfor the future, even if these land-use remediation measures werefully implemented, a recovery of GBR coral reefs may not be sus-tainable if climate change follows the worst scenario (Kleypaset al., 2006; Veron, 2008; Fine and Tchernov, 2007; Jokiel et al.,2008; De’ath et al., 2009; Bohensky et al., 2011), a prediction sup-ported by the HOME model (Fig. 3). The interplay between the localscale in terms of catchment discharges and the global scale interms of climate change determines the various trajectories forthe predicted, future coral cover in this century. If catchment dis-charges of nutrients and fine sediment were not halved at theGBR catchment scale (note that for fine sediments this is a greatertarget – 50%, than that adopted in Reef Plan – a 20% reduction by2020), coral cover is predicted to keep decreasing and to finally col-lapse by 2070 if climate change is not addressed globally (scenario

1 + A in Fig. 3), but to stabilize at about 15–20% if climate change isaddressed globally (scenario 1 + B in Fig. 3). If these catchment dis-charges were halved (scenario 2), coral cover is predicted to in-crease to about 35% before either collapsing if climate change isnot addressed globally (scenario 2 + A in Fig. 3) but to stabilize ina range between 25 and 35% (scenario 2 + B in Fig. 3), which isroughly the present value, if climate change was addressed glob-ally. The reason for the future fluctuations in coral cover in sce-nario 2 + B is a predicted future crown-of-thorns starfishinfestation, which the model suggests would be suppressed onlyif the nutrient discharge from catchments was further decreasedby a factor of two (i.e. a factor of four from present target values)and future anthropogenically driven outbreaks of crown-of-thornsdo not occur.

7. Conclusions

While the residence times of water in the GBR lagoon may beshort, from 15 to 365 days, we suggest the residence times of finesediments, reactive nitrogen and phosphorus, PSII herbicides andtrace metals are highly likely to be considerably greater than theresidence time of water. Our estimates of these residence timesare summarized in Table 1. Based on our best estimates from theavailable data, the residence times of these pollutants within theGBR lagoon will be years to several decades. Fine sediments haveresidence times in the order of decades, during which they remainavailable for resuspension and thus increase turbidity. This lastsuntil waves winnow the fine sediment away from shallow reefsand until the rest of the sediment consolidates, is stored in man-grove forests or transported to deep water. Nitrogen and phospho-rus in the forms of reactive N and reactive P are stored in the GBRfor years in the mobile sediment, benthic biota and water columnbiota, particulate matter and solutes. The main mechanism of lossof N and P is not flushing from the lagoon but processes such asdenitrification and P burial. Photosystem II herbicides such as diu-ron and atrazine are also stored in the lagoon possibly by cyclingthrough the sediment and water column compartments. It appearsthey are primarily removed by chemical (including photolysis) andbiological degradation. Non-conservative trace metals are storedfor very long periods (>50 years) in lagoon sediments and biota,the only possible removal mechanism for trace metals is deepburial.

These conclusions refute the suggestion that pollutant resi-dence times are strongly linked to water residence times and thatsolutes and pollutants are quickly flushed from the GBR lagoon as

276 J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279

implied in the title of the paper by Wang et al. (2007) – ‘‘Flushingtime of solutes and pollutants in the central Great Barrier Reef la-goon, Australia’’ which was based on the premise that ‘solutes andpollutants’ behave in a conservative mixing fashion and are not af-fected by non-conservative processes such as flocculation, settlingor biological uptake. The long residence times of these pollutantsmake it possible for undesirable effects on GBR ecosystems to oc-cur. Brodie et al. (2011), De’ath and Fabricius (2010), Fabriciuset al. (2005, 2010), and McKenzie et al. (2010) have found delete-rious effects on the inshore GBR reefs and seagrass beds from in-creased riverine inputs of nutrients, sediments, and pesticidesarising from human activities in the adjacent catchment area.

Because of the high oceanographic connectivity on the mid toouter shelf of the GBR (as shown for fish larvae by James et al.(2002)) and the presence of healthy reefs within a distance of tensto hundreds kilometers, recruitment of larvae (both coral and fish)to impacted reefs on the mid to outer shelf should readily promotereef regrowth if water and substrate quality were recovered bycatchment remediation. However, inshore reefs are poorly con-nected due to their small size, small numbers, location in poorlyflushed embayments, long distances between reef groups, andminimal connectivity with mid to outer shelf reefs (Wolanskiet al., 2004), and thus the recruitment of coral larvae would bemuch slower if water and substrate quality recovered. Thus, tothe question ‘‘How long will it take to improve water and sedimentquality to the extent required for reef recovery following catch-ment remediation measures?’’, the answer is probably severaldecades.

References

Alexander, J., Fielding, C.R., Pocock, G.D., 1999. Flood behaviour of the BurdekinRiver, tropical north Queensland, Australia. In: Marriott, S.B., Alexander, J. (Eds.),Floodplains Interdisciplinary Approaches. Geological Society, London, pp. 27–40, Special Publications 163.

Alibert, C., Kinsley, L., Fallon, S.J., McCulloch, M.T., Berkelmans, R., McAllister, F.,2003. Source of trace element variability in Great Barrier Reef corals affected bythe Burdekin flood plumes. Geochim. Cosmochim. Acta 67, 231–246.

Alongi, D.M., McKinnon, A.D., 2005. The cycling and fate of terrestrially-derivedsediment and nutrients in the coastal zone of the Great Barrier Reef. Mar. Pollut.Bull. 51, 239–253.

Alongi, D.M., Pfitzner, J., Trott, L.A., 2006. Deposition and cycling of carbon andnitrogen in carbonate mud of the lagoons of Arlington and Sudbury Reefs, GreatBarrier Reef. Coral Reefs 25, 123–143.

Andutta, F., Ridd, P.V., Wolanski, E., 2011. Dynamics of hypersaline coastal waters inthe Great Barrier Reef. Estuar. Coast. Shelf Sci. 94, 299–305.

Angel, B.M., Hales, L.T., Simpson, S.L., Apte, S.C., Chariton, A.A., Shearer, D.A., Jolley,D.F., 2010. Spatial variability of cadmium, manganese, nickel and zinc in thePort Curtis Estuary, Queensland, Australia. Mar. Freshwater Res., 170–183, 61.

Ayukai, T., 1995. Retention of phytoplankton and planctonic microbes on coral reefswithin the Great Barrier Reef, Australia. Coral Reefs 14, 141–147.

Bainbridge, Z., Wolanski, E., Alvarez-Romero, J., Lewis, S., Brodie, J., 2012. Finesediment and nutrient dynamics related to particle size and floc formation in aBurdekin River flood plume, Australia. Marine Pollution Bulletin 65, 236–248.

Bell, P.R.F., Elmetri, I., Uwins, P., 1999. Nitrogen fixation by Trichodesmium spp. Inthe central and northern Great Barrier Reef lagoon: relative importance of thefixed-nitrogen load. Mar. Ecol. Prog. Ser. 186, 119–126.

Belperio, A.P., 1983. Terrigenous sedimentation in the central Great Barrier Reeflagoon: a model from the Burdekin region. BMR J. Geo. Geophys. 8, 179–190.

Black, K.P., 1993. The relative importance of local retention and interreef dispersalof neutrally buoyant material on coral reefs. Coral Reefs 12, 43–53. doi:10.1007/BF00303783.

Bohensky, E., Butler, J.R.A., Costanza, R., Bohnet, I., Delisle, A., Fabricius, K., Gooch,M., Kubiszewski, I., Lukacs, G., Pert, P., Wolanski, E., 2011. Future makers orfuture takers? A scenario analysis of climate change and the Great Barrier Reef.Global Environ. Change 21, 876–893.

Bostock, H.C., Brooke, B.P., Ryan, D.A., Hancock, G., Pietsch, T., Packett, B., Harle, K.,2007. Holocene and modern sediment storage in the subtropical macrotidalFitzroy River estuary, south-east Queensland, Australia. Sed. Geol. 201, 321–340. doi:10.1016/J.SEDGEO.2007.07.001.

Brady, B.A., Johns, B.R., Smith, D.J., 1994. Trace metal geochemical association insediments from the Cairns Region of the Great Barrier Reef, Australia. Mar.Pollut. Bull. 28, 230–234.

Brinkman, R.M., Wolanski, E.J., Deleersnijder, E., McAllister, F.A., Skirving, W.J., 2002.Oceanic inflow from the Coral Sea into the Great Barrier Reef. Estuar. Coast.Shelf Sci. 54, 655–668.

Brinkman, R., Wolanski, E., Spagnol, S., 2004. Field and model studies of thenepheloid layer in coastal waters of the Great Barrier reef, Australia. In: Jirka,G.H., Uijttewaal, W.S.J. (Eds.), ‘‘Shallow Flows’’. A Balkema Publishers, Leiden, p.672, pp. 225–229.

Brodie, J.E., Mitchell, A. 1992. Nutrient composition of the January 1991 FitzroyRiver plume. In: Workshop on the Impacts of Flooding, GBRMPA WorkshopSeries No. 17, GBRMPA, Townsville, pp.56–74

Brodie, J.E., Faithful, J.W., Cullen, K. 2004. Community water quality monitoring inthe Burdekin River catchment and estuary, 2002-2004. Report 04/15, AustralianCentre for Tropical Freshwater Research, James Cook University, Townsville.

Brodie, J., De’ath, G., Devlin, M., Furnas, M., Wright, M., 2007. Spatial and temporalpatterns of near-surface chlorophyll a in the Great Barrier Reef lagoon. Mar.Freshwater Res. 58, 342–353.

Brodie, J.E., Schroeder, T., Rohde, K., Faithful, J.W., Masters, B., Dekker, A., Brando, V.,Maughan, M., 2010. Dispersal of suspended sediments and nutrients in theGreat Barrier Reef lagoon during river discharge events: conclusions fromsatellite remote sensing and concurrent flood plume sampling. Mar. FreshwaterRes. 61, 651–664.

Brodie, J.E., Devlin, M., Haynes, D., Waterhouse, J., 2011. Assessment of theeutrophication status of the Great Barrier Reef lagoon (Australia).Biogeochemistry 106, 281–302. doi:10.1007/s10533-010-9542-2.

Brodie, J.E., Kroon, F.J., Schaffelke, B., Wolanski, E.C., Lewis, S.E., Devlin, M.J., Bohnet,I.C., Bainbridge, Z.T., Waterhouse, J., Davis, A.M., 2012. Terrestrial pollutantrunoff to the Great Barrier Reef: An update of issues, priorities and managementresponses. Mar. Pollut. Bull 65, 81–100.

Brooke, B., Ryan, D., Pietsch, T., Olley, J., Douglas, G., Packett, R., Radke, L., Flood, P.,2008. Influence of climate fluctuations and changes in catchment land use onLate Holocene and modern beach-ridge sedimentation on a tropical macrotidalcoast: Keppel Bay, Queensland, Australia. Mar. Geol. 251, 195–208.

Bronk, D.A., 2002. Dynamics of DON. In: Hansell, D.A., Carlson, C.A. (Eds.),Biogeochemistry of marine dissolved organic matter. Academic Press, SanDiego, pp. 153–249.

Bronk, D.A., See, J.H., Bradley, P., Killberg, L., 2006. DON as a source of bioavailablenitrogen for phytoplankton. Biogeosciences Discussions 3, 1247–1277.

Bruno, J.F., Selig, E.R., 2007. Regional decline of coral cover in the Indo-Pacific:timing, extent, and subregional comparisons. PLoS ONE 2 (8), e711.doi:10.1371/journal.pone.0000711.

Brunskill, G.B., Zagorskis, I., Pfitzner, J., 2002. Carbon burial rates in sediments and acarbon mass balance of the Herbert River region of the Great Barrier Reefcontinental shelf, North Queensland. Estuar. Coast. Shelf Sci. 54, 677–700.

Bryce, S., Larcombe, P., Ridd, P.V., 1998. The relative importance of landward-directed tidal sediment transport versus freshwater flood events in theNormanby River estuary Cape York Peninsula Australia. Mar. Geol. 149, 55–78.

Burgin, A.J., Hamilton, S.K., 2007. Have we overemphasized denitrification inaquatic ecosystems: a review of nitrate removal pathways. Front. Eco. Environ.5, 89–96.

Chongprasith, P. 1992. Nutrient release and nitrogen transformations resulting fromresuspension of Great Barrier Reef shelf sediments. Ph.D. Thesis, James CookUniversity, Townsville, pp. 274

Choukroun, S., Ridd, P.V., Brinkman, R., McKinna, L.I.W., 2010. On the surfacecirculation in the western Coral Sea and residence times in the Great BarrierReef. J. Geophys. Res. 115, C06013. doi:10.1029/2009JC005761.

Conley, D.J., Paerl, H.W., Howarth, R.W., Boesch, D.F., Seitzinger, S.P., Havens, K.E.,Lancelot, C., Likens, G.E., 2009. Controlling eutrophication nitrogen andphosphorus. Science 323, 1014–1015.

Cooper, M., Shields, G., Faithful, J., Zhao, J., 2006. Using Sr/Nd isotopic ratios todefine sediment sources in the Burdekin Falls Dam, Queensland, Australia.Geochim. Cosmochim. Acta 70, A112.

Costanza, R., Bohensky, E., Butler, J., Bohnet, I., Delisle, A., Fabricius, K., Gooch, M.,Kubiszewski, I., Lukacs, G., Pert, P., Wolanski, E. 2011. A scenario analysis ofclimate change and ecosystem services for the Great Barrier Reef. Chapter 16 inVolume 12: Ecological Economics of Estuaries and Coasts, (eds., M. van den Beltand R. Costanza) in the Treatise on Estuarine and Coastal Science (Series eds., E.Wolanski, and D. McLusky), Elsevier.

Currie, B.R., Johns, R.B., 1989. An organic geochemical analysis of terrestrialbiomarkers in a transect of the Great Barrier Reef lagoon. Aust. J. Mar. Freshwat.Res. 40, 275–285.

Dagg, M., Benner, R., Lohrenz, S., Lawrence, D., 2004. Transformation of dissolvedand particulate materials on continental shelves influenced by large rivers:plume processes. Cont. Shelf Res. 24, 833–858.

Davies, P., Eyre, B.D., 2005. Estuarine modification of nutrient and sediment exportsto the Great Barrier Reef Marine Park from the Daintree and Annan Rivercatchments. Mar. Pollut. Bull. 51, 174–185. doi:10.1016/j.marpolbul.2004.11.008.

Davis, A.M., Lewis, S.E., Bainbridge, Z.T., Brodie, J.E., Glendenning, L., Turner, R.,2012. Dynamics of herbicide transport and partitioning under event flowconditions in the lower Burdekin region, Australia. Marine Pollution Bulletin 65,182–193.

De’ath, G., Fabricius, K.E. 2008. Water Quality of the Great Barrier Reef:Distributions, Effects on Reef Biota and Trigger Values for the Protection ofEcosystem Health, Research Publication No. 89. Great Barrier Marine ParkAuthority, Townsville, pp. 104 .

De’ath, G., Fabricius, K.E., 2010. Water quality as regional driver of coral biodiversityand macroalgal cover on the Great Barrier Reef. Ecol. Appl. 20, 840–850.

Death, G., Lough, J.M., Fabricius, K.E., 2009. Declining coral calcification on the GreatBarrier Reef. Science 323, 116–119.

J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279 277

Deleersnijder, E., Campin, J.M., Delhez, E.J.M., 2001. The concept of age in marinemodelling: I. Theory and preliminary model results. J. Mar. Syst. 28, 229–267.

Denton, G.R.W., Burdon-Jones, C., 1986a. Trace metals in surface water from theGreat Barrier Reef. Mar. Pollut. Bull. 17, 96–98.

Denton, G.R.W., Burdon-Jones, C., 1986b. Trace metals in algae from the GreatBarrier Reef. Mar. Pollut. Bull. 17, 98–107.

Denton, G.R.W., Marsh, H., Heinsohn, G.E., Burdon-Jones, C., 1980. The unusualmetal status of the Dugong Dugong dugon. Mar. Biol., 201–219.

Devlin, M., Brodie, J., 2005. Terrestrial discharge into the Great Barrier Reef Lagoon:nutrient behaviour in coastal waters. Mar. Pollut. Bull. 51, 9–22.

Devlin, M.J., Schaffelke, B., 2009. Spatial extent of riverine flood plumes andexposure of marine ecosystems in the Tully coastal region, Great Barrier Reef.Mar. Freshwater Res. 60, 1109–1122.

Devlin, M., Waterhouse, J., Taylor, J., Brodie, J. 2001. Flood plumes in the GreatBarrier Reef: spatial and temporal patterns in composition and distribution.GBRMPA Research Publication No 68, Great Barrier Reef Marine Park Authority,Townsville, Queensland, Australia.

Devlin, M.J., McKinna, L.I.W., Alvarez-Romero, J.G., Abott, B., Harkness, P., Brodie, J.,2012. Mapping the pollutants in surface river plume waters in the Great BarrierReef. Australia. Mar. Pollu. Bull 65, 224–235.

Doherty, G.B., Coomans, D., Brunskill, G.J., 2000. Modelling natural and enhancedtrace metal concentrations in sediments of Cleveland Bay, Australia. Mar.Freshwater Res. 51, 739–747.

Douglas, G., Caitcheon, G., Palmer, M., 2009. Sediment source identification andresidence times in the Maroochy River estuary, southeast Queensland,Australia. Env. Geol. 57, 629–639.

Duke, N.C., Wolanski, E., 2001. Muddy coastal waters and depleted mangrovecoastlines - depleted seagrass and coral reefs. In: Wolanski, E. (Ed.),Oceanographic Processes of Coral Reefs: Physical and Biological Links in theGreat Barrier Reef. CRC Press, Boca Raton, Florida, p. 356, pp. 77–91.

Esslemont, G., 2000. Heavy metals in seawater, marine sediments and corals fromthe Townsville section, Great Barrier Reef Marine Park, Queensland. Mar. Chem.71, 215–231.

Esslemont, G., Russei, R.A., Maher, W.A., 2004. Coral record of harbour dredging:Townsville, Australia. J. Mar. Syst. 52, 51–64.

Fabricius, K.E., De’ath, G., McCook, L., Turak, E., Williams, D.McB., 2005. Changes inalgal, coral and fish assemblages along water quality gradients on the inshoreGreat Barrier Reef. Mar. Pollut. Bull. 51, 384–398.

Fabricius, K.E., Okaji, K., De’ath, G., 2010. Three lines of evidence to link outbreaks ofthe crown-of thorns seastar Acanthaster planci to the release of larval foodlimitation. Coral Reefs 29, 593–605.

Faithful, J.W., Griffiths, D.J., 2000. Turbid flow through a tropical reservoir (LakeDalrymple, Queensland, Australia): Responses to a summer storm event. Lakes -@@- Reservoirs: Research and Management. 5, 231–247.

Fielding, C.R., Alexander, J., McDonald, R., 1999. Sedimentary facies from ground-penetrating radar surveys of the modern, upper Burdekin River of northQueensland, Australia: consequences of extreme discharge fluctuations. SpecialPublications International Association Sedimentologists 28, 347–362.

Fielding, C.R., Trueman, J.D., Alexander, J., 2006. Holocene depositional history of theBurdekin River delta of northeastern Australia: a model for a low-accommodation, highstand delta. J. Sedimen. Res. 76, 411–428.

Fine, M., Tchernov, D., 2007. Scleractinian coral species survive and recover fromdecalcification. Science 315, 1811.

Froelich, P.N., 1988. Kinetic control of dissolved phosphate in natural rivers andestuaries: A primer on the phosphate buffer mechanism. Limnol. Oceanogr. 33,649–668.

Furnas, M.J. 2003. Catchments and Corals: Terrestrial Runoff to the Great BarrierReef. Australian Institute of Marine Science and CRC Reef, Townsville, Australia,pp.334.

Furnas, M.J., Mitchell, A.W., Skuza, M.S. 1997. Shelf-scale nitrogen and phosphorusbudgets in the central Great Barrier Reef (16-19o S). 1:809-814. In: Proceedingsof the 8th International Coral Reef Symposium, Panama, 24-29 June 1996.Smithsonian Tropical Research Institute.

Furnas, M.J., Mitchell, A.W., Skuza, M., Brodie, J., 2005. In the other 90%:Phytoplankton responses to enhanced nutrient availability in the GreatBarrier Reef lagoon. Mar. Pollut. Bull. 51, 253–256.

Furnas, M., Alongi, D., McKinnon, D., Trott, L., Skuza, M., 2011. Regional-scalenitrogen and phosphorus budgets for the northern (140 S) and central (170 S)Great Barrier Reef shelf system. Continental Shelf Research 31, 1967–1990.

Gagan, M.K., Sandstrom, M.W., Chivas, A.R., 1987. Restricted terrestrial carbon inputto the continental shelf during Cyclone Winifred: implications for terrestrialrun-off to the Great Barrier Reef Province. Coral Reefs 6, 113–119.

Gibbs, R.J., 1993. Metals of the bottom muds in Townsville Harbor, Australia.Environ. Pollut., 81: 297–300.

Hancock, G.J., Webster, I., Stieglitz, T.C. 2006. Horizontal mixing of Great BarrierReef waters: Offshore diffusivity determined from radium isotope distribution.Journal of Geophysical Research. 111, (c12), pp. C12019.

Haynes, D., Ralph, P., Prange, J., Dennison, W., 2000. The impact of the herbicidediuron on photosynthesis in three species of tropical seagrass. Mar. Pollut. Bull.41, 288–293.

Haynes, D., Johnson, J.E., 2000. Organochlorine, heavy metal and polyaromatichydrocarbon pollutant concentrations in the Great Barrier Reef (Australia)environment: a review. Mar. Pollut. Bull. 41, 267–278.

Hoegh-Guldberg, O., 1994. Uptake of dissolved organic matter by larval stage of thecrown-of-thorns starfish Acanthaster planci. Mar. Biol. 120, 55–64.

Howarth, R., Jensen, H., Marino, R., Postma, H. 1995. Transport to and processing ofphosphorus in near-shore and oceanic waters (pp 323-345) In: Tiessen H. (Ed.),Phosphorus in the Global Environment 54 Wiley, Chichester, pp. 323–345.

Howarth, R., Chan, F., Conley, D.J., Garnier, J., Doney, S.C., Marino, R., Billen, G., 2011.Coupled biogeochemical cycles: eutrophication and hypoxia in temperateestuaries and coastal marine ecosystems. Front. Ecol.Environ. 9, 18–26.

Hughes, T.P., Bellwood, D.R., Baird, A.H., Brodie, J., Bruno, J.F., Pandolfi, J.M., 2011.Shifting base-lines, declining coral cover, and the erosion of reef resilience:comment on Sweatman et al. (2011). Coral Reefs 30, 653–660.

Hunter, C.L., Evans, C.W., 1995. Coral Reefs in Kaneohe Bay, Hawaii: two centuries ofwestern influence and two decades of data. Bull. Mar. Sci. 57, 501–515.

James, M.K., Armsworth, P.R., Mason, L.B., Bode, L., 2002. The structure of reef fishmetapopulations: Modelling larval dispersal and retention patterns. Proc. Roy.Soc. Lon. Ser. B 269 (1505), 2079–2086. doi:10.1098/rspb.2002.2128.

Jickells, T.D., 1998. Nutrient biogeochemistry of the coastal zone. Science 281, 217–222.

Jokiel, P., Rodgers, K.S., Kuffner, I.B., Andersson, A.J., Cox, E.F., Mackenzie, F.T., 2008.Ocean acidification and calcifying reef organisms: a mesocosm investigation.Coral Reefs 27, 473–478.

Johns, R.B., Brady, B.A., Butler, M.S., Dembitsky, V.M., Smith, J.D., 1994. Organicgeochemical and geochemical studies of inner Great Barrier Reef sediments. IV.Identification of terrigenous and marine sourced inputs. Org. Geochem. 21,1027–1035.

Jones, M.-A., Stauber, J.L., Apte, S.C., Simpson, S.L., Vincente-Beckett, V., Johnson, R.,Duivenvoorden, L., 2005. risk assessment approach to contaminants in PortCurtis, Queensland, Australia. Mar. Pollut. Bull. 51, 448–458. doi:10.1016/J.MARPOLBUL.2004.10.021.

Kennedy, K., Schroeder, T., Shaw, M., Haynes, D., Lewis, S., Bentley, C., Paxman, C.,Carter, S., Brando, V., Bartkow, M., Hearn, L., Mueller, J., 2012. Long termmonitoring of photosystem II herbicides – Correlation with remotely sensedfreshwater extent to monitor changes in the quality of water entering the GreatBarrier Reef, Australia. Marine Pollution Bulletin 65, 292–305.

King, B., McAllister, F., Wolanski, E., Done, T., Spagnol, S., 2001. River plumedynamics in the central Great Barrier Reef. In: Wolanski, E. (Ed.), OceanographicProcesses of Coral Reefs: Physical and Biological Links in the Great Barrier Reef.CRC Press, Boca Raton, Florida, pp. 145–160.

Kingsford, M.J., Wolanski, E., 2008. Oceanography. In: Hutchings, P., Kingsford, M.,Hoegh-Guldberg, O. (Eds.), The Great Barrier Reef. CSIRO Publishing andSpringer, Collingwood and Dordrecht, pp. 28–39.

Kinsey, D.W., 1988. Coral reef system response to some natural and anthropogenicstresses. Galaxea 7, 113–128.

Kleypas, J.A., Feely, R.A., Fabry V.J., Langdon, C., Sabine, C.L., Robbins, L.L. 2006.Impacts of ocean acidification on coral reefs and other marine calcifiers: a guidefor future research, report of a workshop held 18-20 April 2005, St. Petersburg,FL, sponsored by NSF, NOAA, and the US Geological Survey. http://www.ucar.edu/communications/Final_acidification.pdf.

Krom, M.D., Berner, R.A., 1980. Adsorption of phosphate in anoxic marinesediments. Limnol. Oceanogr. 25, 797–806.

Kroon, F.J., 2012. Towards ecologically relevant targets for river pollutant loads tothe Great Barrier Reef. Mar. Pollut. Bull 65, 261–266.

Kroon, F.J., Kuhnert, K.M., Henderson, B.L., Wilkinson, S.N., Kinsey-Henderson, A.,Brodie, J.E., Turner, R.D.R., 2012. River loads of suspended solids, nitrogen,phosphorus and herbicides delivered to the Great Barrier Reef lagoon. MarinePollution Bulletin 65, 167–181.

Lambeck, A., Woolfe, K.J., 2000. Composition and textural variability along the 10misobath, Great Barrier Reef: evidence for pervasive northward sedimenttransport. Aust. J. Earth Sci. 47, 327–335.

Lambrechts, J., Humphrey, C., McKinna, L., Gourge, O., Fabricius, K., Mehta, A., Lewis,S., Wolanski, E., 2010. The importance of wave-induced bed fluidisation in thefine sediment budget of Cleveland Bay, Great Barrier Reef. Estuar. Coast. ShelfSci. 89, 154–162.

Larcombe, P., Woolfe, K.J., 1999. Increased sediment supply to the Great Barrier Reefwill not increase sediment accumulation at most coral reefs. Coral Reefs 18,163–169.

Larcombe, P., Carter, R.M., 2004. Cyclone pumping, sediment partitioning and thedevelopment of the Great Barrier Reef shelf system: a review. Quatern. Sci. Rev.23, 107–135.

Larcombe, P., Ridd, P.V., Prytz, A., Wilson, B., 1995. Factors controlling suspendedsediment on inner-shelf coral reefs, Townsville, Australia. Coral Reefs 14, 163–171.

Lewis, S., Shields, G., Kamber, B., Lough, J., 2007. A multi-trace element coral recordof land-use changes in the Burdekin River catchment, NE Australia. Palaeogeo.Palaeoclim. Palaeoecol. 246, 471–487.

Lewis, S.E., Brodie, J.E., Bainbridge, Z.T., Rohde, K.W., Davis, A.M., Masters, B.L.,Maughan, M., Devlin, M.J., Mueller, J.F., Schaffelke, B., 2009. Herbicides: a newthreat to the Great Barrier Reef. Environ. Pollut. 157, 2470–2484.

Lewis, S. E., Bainbridge, Z. T., Sherman, B. S., Brodie, J. E., Cooper, M., 2009b. Thetrapping efficiency of the Burdekin Falls Dam: Estimates from a three-yearmonitoring program. Report to the Marine and Tropical Sciences ResearchFacility. Reef and Rainforest Research Centre Limited, Cairns and AustralianCentre for Tropical Freshwater Research (ACTFR), Townsville 31pp. http://www.rrrc.org.au/publications/downloads/372-JCU-Lewis-S-et-al-2009-Burdekin-Dam-trapping-efficiency.pdf

Lewis, S.E., Brodie, J.E., McCulloch, M.T., Malella, J., Jupiter, S., Stuart-Williams, H.,Lough, J., Matson, E., 2012. An assessment of an environmental gradient using

278 J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279

coral geochemical records, Whitsunday Islands, Great Barrier Reef, Australia.Marine Pollution Bulletin 65, 306–319.

Luick, J.L., Mason, L., Hardy, T., Furnas, M.J., 2007. Circulation in the Great BarrierReef Lagoon using numerical tracers and in situ data. Cont. Shelf Res. 27, 757–778.

Margvelashvili, N., Herzfeld, M., Webster, I. 2006. Modelling of fine sedimenttransport in Fitzroy Estuary and Keppel Bay. Report 39 to CRC for Coastal Zone,Estuary and Waterway Management, Indooroopilly. http://www.ozcoasts.org.au/search_data/crc_rpts.jsp#no39.

Mathews, E.J., Heap, A.D., Woods, M. 2007. Inter-reefal seabed sediments andgeomorphology of the Great Barrier Reef, a spatial analysis. GeoscienceAustralia, Record 2007/09, pp. 140.

Maxwell, W.G.H., 1968. Atlas of the Great Barrier Reef. Elsevier, Amsterdam.Mayer, L.M., Keil, R.G., Macko, S.A., Joye, S.B., Ruttenberg, K.C., Aller, R.C., 1998.

Importance of suspended particulates in riverine delivery of bioavailablenitrogen to coastal zones. Global Biogeochem. Cycles 12, 573–579.

McCulloch, M., Pailles, C., Moody, P., Martin, C.E., 2003a. Tracing the source ofsediment and phosphorus into the Great Barrier Reef lagoon. Earth Planet. Sci.Lett. 210, 249–258.

McCulloch, M.T., Fallon, S., Wyndham, T., Hendy, E., Lough, J., Barnes, D., 2003b.Coral record of increased sediment flux to the inner Great Barrier Reef sinceEuropean settlement. Nature 421, 727–730.

McKenzie, L.J., Unsworth, R.K.F., Waycott, M. 2010. Reef Rescue Marine MonitoringProgram: Intertidal Seagrass, Annual Report for the sampling period 1stSeptember 2009 - 31st May 2010. Fisheries Queensland, Cairns pp. 136.

McKinnon, A.D., Thorrold, S.R., 1993. Zooplankton community structure andcopepod egg production in coastal waters of the central Great Barrier ReefLagoon. J. Plankton Res. 15, 1387–1411.

Middelburg, J.J., Herman, P.M.J., 2007. Organic matter processing in tidal estuaries.Mar. Chem. 106, 127–147.

Monbet, Ph., Brunskill, G.J., Zagorskis, I., Pfitzner, J., 2007. Phosphorus speciation inthe sediment and mass balance for the central region of the Great Barrier Reefcontinental shelf (Australia). Geochim. Cosmochim. Acta 71, 2762–2779.

Monsen, N.E., Cloern, J.E., Lucas, L.V., 2002. A comment on the use of flushing time,residence time, and age as transport time scales. Limnol. Oceanogr. 47, 1545–1553.

Mortimer, M.R., 2000. Pesticide and trace metal concentrations in Queenslandestuarine crabs. Mar. Pollut. Bull. 41, 7–12.

Muller, J., Wust, R.A.J., Hearty, P.J., 2006. Sediment transport along an artificialshoreline: ‘‘The Strand’’ Townsville NE-Queensland, Australia. Estuar. Coast.Shelf Sci. 66, 204–210.

Negri, A.P., Mortimer, M., Carter, C., Müller, J.F., 2009. Persistent organochlorinesand metals in estuarine mud crabs of the Great Barrier Reef. Mar. Pollut. Bull.58, 765–786.

Neil, D.T., Orpin, A.R., Ridd, P.V., Yu, B., 2002. Sediment yield and impacts from rivercatchments to the Great Barrier Reef Lagoon. Marine Freshwater Research. 53,733–752.

Oliveira, A., Baptista, A.M., 1997. Diagnostic modeling of residence times inestuaries. Water Resour. Res. 33, 1935–1946.

O’Neil, J.M., Capone, D.G., 2008. Nitrogen Cycling on Coral Reefs. In: Capone, D.G.,Carpenter, E.J., Bronk, D.A., Mulholland, M.R. (Eds.), Nitrogen in the MarineEnvironment. Elsevier, Press, pp. 937–977, Chapter X.

Orpin, A.R., Brunskill, G.J., Zagorskis, I., Woolfe, K.J., 2004. Patterns of mixedsiliciclastic-carbonate sedimentation adjacent to a large dry-tropics river on thecentral Great Barrier Reef shelf, Australia. Aust. J. Earth Sci. 51, 665–683.

Paerl, H.W., 2009. Controlling Eutrophication along the Freshwater–MarineContinuum: Dual Nutrient (N and P) Reductions are Essential. EstuariesCoasts 32, 593–601.

Radke, L.C., Ford, P.W., Webster, I.T., Atkinson, I., Douglas, G., Oubelkheir, K., Robson,B., Brooke, B., 2010. Biogeochemical zones within a macrotidal, dry- tropicalfluvial-marine transition area: a dry-season perspective. Aquat. Geochem. 16,1–29. doi:10.1007/s10498-009-9070-7.

Reef Plan. Department of the Premier and Cabinet 2003. Reef Water QualityProtection Plan; for catchments adjacent to the Great Barrier Reef WorldHeritage Area. Queensland Department of Premier and Cabinet, Brisbane.

Reef Plan. Department of the Premier and Cabinet 2009. Reef Water QualityProtection Plan 2009: For the Great Barrier Reef World Heritage Area andadjacent catchments, Queensland Department of Premier and Cabinet, Brisbane.http://www.reefplan.qld.gov.au/library/pdf/paddock-to-reef.pdf

Reichelt, A.J., Jones, G.B., 1994. Trace metals as tracers of dredging activity inCleveland Bay- field and laboratory studies. Aust. J. Mar. Freshwat. Res. 45,1237–1257.

Richmond, R.H., Wolanski, E. 2011. Coral reef research: past efforts and futurehorizons. In Dubinsky, Z. (Ed.), Corals and Coral Reefs. Springer Science. in press.

Risk, M.J., Sammarco, P.W., Schwarcz, H.P., 1994. Cross-continental shelf trends ind13C in coral on the Great Barrier Reef. Mar. Ecol. Prog. Ser. 106, 121–130.

Ryan, D.A., Brooke, B.P., Bostock, H.C., Radke, L.C., Siwabessy, P.J.W., Margvelashvili,N., Skene, D., 2007. Bedload sediment transport dynamics in a macrotidalembayment, and implications for export to the southern Great Barrier Reefshelf. Mar. Geol. 240, 197–215.

Sammarco, P.W., Risk, M.J., Schwarcz, H.P., Heikoop, J.M., 1999. Cross-continentalshelf trends in coral d15N on the Great Barrier Reef: further consideration of thereef nutrient paradox. Mar. Ecol. Prog. Ser. 180, 131–138.

Schaffelke, B., 1999. Particulate organic matter as an alternative nutrient source fortropical Sargassum species (Fucales, Phaeophyceae). J. Phycol. 35, 1150–1157.

Schroeder, T.h., Devlin, M., Brando, V.E., Dekker, A.G., Brodie, J., Clementson, L.,McKinna, L., 2012. Inter-annual variability of wet season freshwater plumeextent in the Great Barrier Reef lagoon from satellite ocean colour observations.Marine Pollution Bulletin 65, 210–223.

Seitzinger, S.P., 1988. Denitrification in freshwater and coastal marine ecosystems:ecological and geochemical significance. Limnol. Oceanogr. 33, 702–724.

Seitzinger, S., Sanders, R., 1997. Contribution of dissolved organic nitrogen fromrivers to estuarine eutrophication. Mar. Ecol. Prog. Ser. 159, 1–12.

Seitzinger, S.P., Sanders, R.W., Styles, R., 2002. Bioavailability of DON from Naturaland Anthropogenic Sources to Estuarine Plankton. Limnol. Oceanogr. 47, 353–366.

Seitzinger, S.P., Harrison, J.A., Dumont, E., Beusen, A.H.W., Bouwman, A.F., 2005.Sources and delivery of carbon, nitrogen, and phosphorus to the coastal zone:An overview of Global Nutrient Export from Watersheds (NEWS) models andtheir application. Global Biogeochem. Cycles 19 (4), GB4501. doi:10.1029/2005GB002606.

Shaw, M., Müller, J.F., 2005. Preliminary evaluation of the occurrence of herbicidesand PAH’s in the Wet Tropics region of the Great Barrier Reef, Australia, usingpassive samplers. Mar. Pollut. Bull. 51, 876–881.

Shaw, M., Furnas, M.J., Fabricius, K., Haynes, D., Carter, S., Eaglesham, G., Mueller,J.F., 2010. Monitoring pesticides in the Great Barrier Reef. Mar. Pollut. Bull. 60,113–122.

Shaw, P.M., Johns, R.B., 1985. Organic geochemical studies of a recent inner GreatBarrier Reef sediment. I. Assessment of input sources. Organic Geochemistry. 8,147–156. doi:10.1016/0146-6380(85)90032-4.

Shaw, P.M., Johns, R.B., 1986. Organic geochemical studies of a recent Inner GreatBarrier Reef sediment. II. Factor analysis of sedimentary organic materials ininput source determinations. Org. Geochem. 9, 237–244. doi:10.1016/0146-6380(86)90096-3.

Sinclair, D.J., 2005. Non-river flood barium signals in the skeletons of corals fromcoastal Queensland, Australia. Earth Planetary Sciences Letters 237, 354–369.

Sinclair, D.J., McCulloch, M.T. 2004. Coral record low mobile barium concentrationsin the Burdekin River during the 1974 flood: evidence for limited Ba supply torivers? Palaeogeography Palaeoclimatology, Palaeoecology. 214, 155-174.

Smith, S.V., Kimmerer, W.J., Laws, E.A., Brock, R.E., Walsh, T.W., 1981. Kaneohe Baysewage diversion experiment: perspectives on ecosystem responses tonutritional perturbation. Pac. Sci. 35, 279–395.

Smith, J., Douglas, G., Radke, L., Palmer, M., Brooke, B., 2008. Fitzroy River Basin,Queensland, Australia. III. Identification of sediment sources in the coastal zone.Environmental Chemistry 5, 231-242. doi.org/10.1071/EN07094.

Spagnol, S., Wolanski, E., Deleersnjider, E., 2001. Steering by coral reef assemblages.pp. 145-160 in E. Wolanski. E. (ed). Oceanographic Processes of Coral Reefs:Physical and Biological Links in the Great Barrier Reef. CRC Press, Boca Raton,Florida, pp. 356.

Stimson, J., Larned, S.T., Conkin, E., 2001. Effects of herbivory, nutrient levels andintroduced algae on the distribution and abundance of the invasive macroalgaDictyosphaeria cavernosa in Kaneohoe Bay, Hawai’i. Coral Reefs 19, 343–357.

Storlazzi, C.D., Jaffe, B.E., 2008. The relative contribution of processes drivingvariability in flow, shear, and turbidity over a fringing coral reef: West Maui,Hawaii. Estuar. Coast. Shelf Sci. 77, 549–564.

Sundby, B., Gobeil, C., Silverberg, N., Mucci, A., 1992. The phosphorus cycle incoastal marine sediments. Limnol. Oceanogr. 37, 1129–1145.

Suzuki, A., Nakamori, T., Kayanne, H., 1995. The mechanism of productionenhancement in coral reef carbonate systems: model and empirical results.Sed. Geol. 99, 259–280.

Sweatman, H., Delean, S., Syms, C., 2011. Assessing loss of coral cover on Australia’sGreat Barrier Reef over two decades, with implications for longer-term trends.Coral Reefs 30, 521–531.

Tappin, A.D., 2002. An examination of the fluxes of nitrogen and phosphorus intemperate and tropical estuaries: current estimates and uncertainties. Estuar.Coast. Shelf Sci. 55, 885–901.

Taylor, S.R., McLennan, S.M., 1985. The continental crust: Its composition andevolution. Blackwell Scientific Publ., Oxford, England, p. 312.

Thorburn, P.J., Wilkinson, S.N., in press. Conceptual frameworks for estimating thewater quality benefits of improved land management practices in largecatchments. Agr. Ecosyst. Environ. doi:10.1016/j.agee.2011.12.021.

Thorrold, S.R., McKinnon, A.D., 1995. Response of larval fish assemblages to ariverine plume in coastal waters of the central Great Barrier Reef lagoon.Limnol. Oceanogr. 40, 177–181.

Turner, R.E., Rabalais, N.N., Nan, Z.Z., 1990. Phytoplankton biomass, production andgrowth limitations on the Huanghe (Yellow) River continental shelf. Cont. ShelfRes. 10, 545–571.

Turner, R.E., Qureshi, N., Rabalais, N.N., Dortch, Q., Justic, R., Shaw, F., Cope, J., 1998.Fluctuating silicate:nitrate ratios and coastal plankton food webs. ProceedingsNational Academy of Sciences U.S.A., 95: 13048–13051.

Ullman, W.J., Sandstrom, M.W., 1987. Dissolved nutrient flux from the nearshoresediments of Bowling Green Bay, Central Great Barrier Reef Lagoon(Australia).Estuar. Coast. Shelf Sci. 24, 289–303.

van der Zee, C., Roevros, N., Chou, L. 2007. Phosphorus speciation, transformationand retention in the Scheldt estuary (Belgium/The Netherlands) from thefreshwater tidal limits to the North Sea, Marine Chemistry. 106, 76-91.doi:10.1016/j.marchem.2007.01.003.

van Oppen M. J. H., Lutz, A., De’ath, G., Peplow, L., Kininmonth, S., 2008. Genetictraces of recent long-distance dispersal in a predominantly self-recruiting coral.PLoS One. 3(10), E3401, doi:10.1371/journal.pone.0003401.

J. Brodie et al. / Marine Pollution Bulletin 65 (2012) 267–279 279

Veron, J.E.N., 2008. A Reef in Time. Harvard University Press, Cambridge. Mas,sachusetts.

Walker, T.A., 1981. Dependence of phytoplankton chlorophyll on bottomresuspension in Cleveland Bay, northern Queensland. Aust. J. Mar. Freshwat.Res. 32, 981–986.

Walker, G.S., Brunskill, G.J. 1996. Detection of anthropogenic and natural mercury insediments from the Great Barrier Reef lagoon. In: Larcombe, P. Woolfe, K.Purdon, R. (eds). Great Barrier Reef: terrigenous sediment flux and humanimpacts second edition. CRC Reef Research Centre, Townsville, pp 155-159.

Walker, G.S., Brunskill, G.J., 1997. Detection of anthropogenic and natural mercuryin sediments from the Great Barrier Reef lagoon. In: Campbell. J. Dalliston, C.(eds). The Great Barrier Reef:. Science, Use and Management, a NationalConference 25-29th November 1996, James Cook University, Townsville,Queensland, Australia Volume 2. Great Barrier Reef Marine Park Authority,Townsville, Australia, pp. 30–33.

Wang, Y., Ridd, P.V., Heron, M.L., Stieglitz, T.C., Orpin, A.R., 2007. Flushing time ofsolutes and pollutants in the central Great Barrier Reef lagoon, Australia. MarineFreshwater Research 58, 778–791. doi:10.1071/MF06148.

Weber, M., Lott, C., Fabricius, K.E., 2006. Sedimentation stress in a scleractinian coralexposed to terrestrial and marine sediments with contrasting physical, organicand geochemical properties. J. of Experimental Marine Biology and Ecology.336, 18–32.

Webster, I.T., Ford, P.W., 2010. Delivery, deposition and redistribution of finesediments within macrotidal Fitzroy Estuary/Keppel Bay: Southern GreatBarrier Reef, Australia. Cont. Shelf Res. 30, 793–805.

Wolanski, E., 1994. Physical Oceanographic Processes of the Great Barrier Reef. CRCPress, Boca Raton, Florida, pp. 194.

Wolanski, E., 2007. Estuarine Ecohydrology. Elsevier, Amsterdam, pp. 157.Wolanski, E., Jones, M., 1981. Physical properties of Great Barrier Reef lagoon waters

near Townsville. I. Effects of Burdekin River Floods. Australian Journal of Marineand Freshwater Research. 32, 305–319.

Wolanski, E., Ridd, P., 1990. Mixing and trapping in Australian tropical coastalwaters. In: Cheng, R.T. (Ed.), ‘‘Residual Currents and Long-term’’, Coastal andEstuarine Studies, vol. 38. Springer-Verlag, New York, pp. 165–183.

Wolanski, E., Spagnol, S., 2000a. Environmental degradation by mud in tropicalestuaries. Reg. Environ. Change 1, 152–162.

Wolanski, E., Spagnol, S., 2000b. Pollution by mud of Great Barrier Reef coastalwaters. J. Coastal Res. 16, 1151–1156.

Wolanski, E., van Senden, D., 1982. Mixing of Burdekin River flood waters in theGreat Barrier Reef. Aust. J. Mar. Freshwat. Res. 34, 49–63.

Wolanski, E., Richmond, R.H., McCook, L., 2004a. A model of the effects of land-based, human activities on the health of coral reefs in the Great Barrier Reef andin Fouha Bay, Guam, Micronesia. J. Mar. Syst. 46, 133–144.

Wolanski, E., Spagnol, S., Williams, D., 2004b. The impact of damming the Ord Riveron the fine sediment budget in Cambridge Gulf, northwestern Australia. J.Coastal Res. 20, 801–807.

Wolanski, E., Moore, K., Spagnol, S., D’Adamo, N., Pattiaratchi, C., 2001. Rapid,human-induced siltation of the macro-tidal Ord River Estuary, WesternAustralia. Estuar. Coast. Shelf Sci. 53, 717–732. doi:10.1006/ecss.2001.0799.

Wolanski, E., Fabricius, K., Spagnol, S., Brinkman, R., 2005. Fine sediment budget onan inner-shelf coral-fringed island, Great Barrier Reef of Australia. Estuar. Coast.Shelf Sci. 65, 153–158.

Wolanski, E., Fabricius, K.E., Cooper, T.F., Humphrey, C., 2008. Wet season finesediment dynamics on the inner shelf of the Great Barrier Reef. Estuar. Coast.Shelf Sci. 77, 755–762.

Woolfe, K.J., Larcombe, P., 1999. Terrigenous sedimentation and coral reef growth: aconceptual framework. Mar. Geol. 155, 331–345.

Wyndham, T., McCulloch, M., Fallon, S., Alibert, C., 2004. High resolution coralrecords of rare earth elements in coastal seawater: biogeochemical cycling anda new environmental proxy. Geochim. Cosmochim. Acta 68, 2067–2080.