Making a Model Meaningful to Coral Reef Managers in a Developing Nation: a Case Study of Overfishing and Rock Anchoring in Indonesia

Abstract: Most of the world's coral reefs line the coasts of developing nations, where impacts from intense and destructive fishing practices form critical conservation issues for managers. Overfishing of herbivorous fishes can cause phase shifts to macroalgal dominance, and fishers’ use of rocks as anchors lowers coral cover, giving further competitive advantage to macroalgae. Overfishing and anchoring have been studied extensively, but the role of their interaction in lowering coral reef resilience has not been quantified formally. We analyzed the combined effects of overfishing and rock anchoring on a range of reef habitat types—varying from high coral and low macroalgae cover to low coral and high macroalgae cover—in a marine park in Indonesia. We parameterized a model of coral and algal dynamics with three intensities of anchoring and fishing pressure. Results of the model indicated that damage caused by rock anchoring was equal to or possibly more devastating to coral reefs in the area than the impact of overfishing. This is an important outcome for local managers, who usually have the funds to distribute less‐damaging anchors, but normally are unable to patrol regularly and effectively enough to reduce the impact of overfishing. We translated model results into an interactive visual tool that allows managers to explore the benefits of reducing anchoring frequency and fishing pressure. The potential consequences of inaction were made clear: the likelihood that any of the reef habitats will be dominated in the future by macroalgae rather than corals depends on reducing anchoring frequency, fishing pressure, or both. The tool provides a platform for strengthened relationships between managers and conservationists and can facilitate the uptake of recommendations regarding resource allocation and management actions. Conservation efforts for coral reefs in developing nations are likely to benefit from transforming model projections of habitat condition into tools local managers can understand and interact with.     

A geological perspective on the degradation and conservation of western Atlantic coral reefs

Continuing coral‐reef degradation in the western Atlantic is resulting in loss of ecological and geologic functions of reefs. With the goal of assisting resource managers and stewards of reefs in setting and measuring progress toward realistic goals for coral‐reef conservation and restoration, we examined reef degradation in this region from a geological perspective. The importance of ecosystem services provided by coral reefs—as breakwaters that dissipate wave energy and protect shorelines and as providers of habitat for innumerable species—cannot be overstated. However, the few coral species responsible for reef building in the western Atlantic during the last approximately 1.5 million years are not thriving in the 21st century. These species are highly sensitive to abrupt temperature extremes, prone to disease infection, and have low sexual reproductive potential. Their vulnerability and the low functional redundancy of branching corals have led to the low resilience of western Atlantic reef ecosystems. The decrease in live coral cover over the last 50 years highlights the need for study of relict (senescent) reefs, which, from the perspective of coastline protection and habitat structure, may be just as important to conserve as the living coral veneer. Research is needed to characterize the geological processes of bioerosion, reef cementation, and sediment transport as they relate to modern‐day changes in reef elevation. For example, although parrotfish remove nuisance macroalgae, possibly promoting coral recruitment, they will not save Atlantic reefs from geological degradation. In fact, these fish are quickly nibbling away significant quantities of Holocene reef framework. The question of how different biota covering dead reefs affect framework resistance to biological and physical erosion needs to be addressed. Monitoring and managing reefs with respect to physical resilience, in addition to ecological resilience, could optimize the expenditure of resources in conserving Atlantic reefs and the services they provide.     

Modelling the dynamics of coral reef macroalgae using a Bayesian belief network approach

Macroalgae are a major benthic component of coral reefs and their dynamics influence the resilience of coral reefs to disturbance. However, the relative importance of physical and ecological processes in driving macroalgal dynamics is poorly understood. Here we develop a Bayesian belief network (BBN) model to integrate many of these processes and predict the growth of coral reef macroalgae. Bayesian belief networks use probabilistic relationships rather than deterministic rules to quantify the cause and effect assumptions. The model was developed using both new empirical data and quantified relationships elicited from previous studies. We demonstrate the efficacy of the BBN to predict the dynamics of a common Caribbean macroalgal genus Dictyota. Predictions of the model have an average accuracy of 55% (implying that 55% of the predicted categories of Dictyota cover were assigned to the correct class). Sensitivity analysis suggested that macroalgal dynamics were primarily driven by top–down processes of grazing rather than bottom–up nutrification. BBNs provide a useful framework for modelling complex systems, identifying gaps in our scientific understanding and communicating the complexities of the associated uncertainties in an explicit manner to stakeholders. We anticipate that accuracies will improve as new data are added to the model.     

化学污染物对珊瑚礁生态系统的影响研究进展

化学污染物是影响珊瑚礁生态系统健康的重要因素之一。近年来,中国沿海地区农业活动、城市工业化以及旅游业发展迅速,珊瑚礁区的环境污染问题日趋严重。珊瑚礁生态系统长期处于化学污染物的联合毒性作用下,生态风险日益增加,已受到国内外研究者的广泛关注。本文综述了该领域的重要研究进展,并从个体、细胞和分子水平重点介绍了化学污染物对珊瑚的影响,主要包括:(1)珊瑚礁对重金属和多环芳烃有明显的富集作用,可以作为该海域化学污染物污染水平的外在反映;(2)化学污染物对珊瑚幼体的影响程度比成体大;(3)抗氧化酶和特定的功能基因可被用作生物标记物(biomarker)来监测珊瑚礁生态系统的健康状况。最后,本文对我国珊瑚礁生态系统未来的研究方向进行了展望,建议在典型的珊瑚礁海域进行长期的生态学监测,并结合室内毒理学实验,筛选出敏感的生物标志物,评价珊瑚礁生态系统可能存在的生态风险,为今后珊瑚礁生态系统的保护和管理提供科学依据。     

Quantifying parameter uncertainty in a coral reef model using Metropolis-Coupled Markov Chain Monte Carlo

Coral reefs are threatened ecosystems, so it is important to have predictive models of their dynamics. Most current models of coral reefs fall into two categories. The first is simple heuristic models which provide an abstract understanding of the possible behaviour of reefs in general, but do not describe real reefs. The second is complex simulations whose parameters are obtained from a range of sources such as literature estimates. We cannot estimate the parameters of these models from a single data set, and we have little idea of the uncertainty in their predictions.We have developed a compromise between these two extremes, which is complex enough to describe real reef data, but simple enough that we can estimate parameters for a specific reef from a time series. In previous work, we fitted this model to a long-term data set from Heron Island, Australia, using maximum likelihood methods. To evaluate predictions from this model, we need estimates of the uncertainty in our parameters. Here, we obtain such estimates using Bayesian Metropolis-Coupled Markov Chain Monte Carlo. We do this for versions of the model in which corals are aggregated into a single state variable (the three-state model), and in which corals are separated into four state variables (the six-state model), in order to determine the appropriate level of aggregation. We also estimate the posterior distribution of predicted trajectories in each case.In both cases, the fitted trajectories were close to the observed data, but we had doubts about the biological plausibility of some parameter estimates. We suggest that informative prior distributions incorporating expert knowledge may resolve this problem. In the six-state model, the posterior distribution of state frequencies after 40 years contained two divergent community types, one dominated by free space and soft corals, and one dominated by acroporid, pocilloporid, and massive corals. The three-state model predicts only a single community type. We conclude that the three-state model hides too much biological heterogeneity, but we need more data if we are to obtain reliable predictions from the six-state model. It is likely that there will be similarly large, but currently unevaluated, uncertainty in the predictions of other coral reef models, many of which are much more complex and harder to fit to real data.     

Diversity and stability of herbivorous fishes on coral reefs

Biodiversity may provide insurance against ecosystem collapse by stabilizing assemblages that perform particular ecological functions (the "portfolio effect"). However, the extent to which this occurs in nature and the importance of different mechanisms that generate portfolio effects remain controversial. On coral reefs, herbivory helps maintain coral dominated states, so volatility in levels of herbivory has important implications for reef ecosystems. Here, we used an extensive time series of abundances on 35 reefs of the Great Barrier Reef of Australia to quantify the strength of the portfolio effect for herbivorous fishes. Then, we disentangled the contributions of two mechanisms that underlie it (compensatory interactions and differential responses to environmental fluctuations ["response diversity"]) by fitting a community-dynamic model that explicitly includes terms for both mechanisms. We found that portfolio effects operate strongly in herbivorous fishes, as shown by nearly independent fluctuations in abundances over time. Moreover, we found strong evidence for high response diversity, with nearly independent responses to environmental fluctuations. In contrast, we found little evidence that the portfolio effect in this system was enhanced by compensatory ecological interactions. Our results show that portfolio effects are driven principally by response diversity for herbivorous fishes on coral reefs. We conclude that portfolio effects can be very strong in nature and that, for coral reefs in particular, response diversity may help maintain herbivory above the threshold levels that trigger regime shifts.     

Translating the 10 golden rules of reforestation for coral reef restoration

Efforts are accelerating to protect and restore ecosystems globally. With trillions of dollars in ecosystem services at stake, no clear framework exists for developing or prioritizing approaches to restore coral reefs even as efforts and investment opportunities to do so grow worldwide. Restoration may buy time for climate change mitigation, but it lacks rigorous guidance to meet objectives of scalability and effectiveness. Lessons from restoration of terrestrial ecosystems can and should be rapidly adopted for coral reef restoration. We propose how the 10 golden rules of effective forest restoration can be translated to accelerate efforts to restore coral reefs based on established principles of resilience, management, and local stewardship. We summarize steps to undertake reef restoration as a management strategy in the context of the diverse ecosystem service values that coral reefs provide. Outlining a clear blueprint is timely as more stakeholders seek to undertake restoration as the UN Decade on Ecosystem Restoration begins.     

A spatial model of growth and competition strategies in coral communities

A discrete spatial simulation model is developed to investigate the type and intensity of biological and physical factors influencing the structure of coral communities. The model represents reproduction, growth, and interspecific competition by coral colonies in terms of “ownership” of space in a plot of reef habitat. Using data for several eastern Pacific coral species, the model reproduces observed changes in species composition and diversity during coral community development. Model results suggest that during early successional stages, or in areas that are frequently disturbed, larval colonization and rapid growth are more important than dominance achieved by extracoelenteric digestion or by growing over another coral in acquiring and maintaining possession of reef substrate. In mature communities that remain undisturbed, dominance is the best competitive strategy. Although the model was developed to study natural and man-induced changes in the community dynamics of coral reefs, it could be adapted to study other sessile organisms where spatial pattern is an important influence on the frequency and outcome of biological interactions.     

Biomass‐based targets and the management of multispecies coral reef fisheries

The failure of fisheries management among multispecies coral reef fisheries is well documented and has dire implications for the 100 million people engaged in these small‐scale operations. Weak or missing management institutions, a lack of research capacity, and the complex nature of these ecosystems have heralded a call for ecosystem‐based management approaches. However, ecosystem‐based management of coral reef fisheries has proved challenging due to the multispecies nature of catches and the diversity of fish functional roles. We used data on fish communities collected from 233 individual sites in 9 western Indian Ocean countries to evaluate changes in the site's functional composition and associated life‐history characteristics along a large range of fish biomass. As biomass increased along this range, fish were larger and grew and matured more slowly while the abundance of scraping and predatory species increased. The greatest changes in functional composition occurred below relatively low standing stock biomass (<600 kg/ha); abundances of piscivores, apex predators, and scraping herbivores were low at very light levels of fishing. This suggests potential trade‐offs in ecosystem function and estimated yields for different management systems. Current fishing gear and area restrictions are not achieving conservation targets (proposed here as standing stock biomass of 1150 kg/ha) and result in losses of life history and ecological functions. Fish in reefs where destructive gears were restricted typically had very similar biomass and functions to young and low compliance closures. This indicates the potentially important role of fisheries restrictions in providing some gains in biomass and associated ecological functions when fully protected area enforcement potential is limited and likely to fail. Our results indicate that biomass alone can provide broad ecosystem‐based fisheries management targets that can be easily applied even where research capacity and information is limited. Of particular value, is our finding that current management tools may be used to reach key ecosystem‐based management targets, enabling ecosystem‐based management in many socioeconomic contexts.     

Acute effects of removing large fish from a near-pristine coral reef

Large animals are severely depleted in many ecosystems, yet we are only beginning to understand the ecological implications of their loss. To empirically measure the short-term effects of removing large animals from an ocean ecosystem, we used exclosures to remove large fish from a near-pristine coral reef at Palmyra Atoll, Central Pacific Ocean. We identified a range of effects that followed from the removal of these large fish. These effects were revealed within weeks of their removal. Removing large fish (1) altered the behavior of prey fish; (2) reduced rates of herbivory on certain species of reef algae; (3) had both direct positive (reduced mortality of coral recruits) and indirect negative (through reduced grazing pressure on competitive algae) impacts on recruiting corals; and (4) tended to decrease abundances of small mobile benthic invertebrates. Results of this kind help advance our understanding of the ecological importance of large animals in ecosystems.     

Coral identity underpins architectural complexity on Caribbean reefs

The architectural complexity of ecosystems can greatly influence their capacity to support biodiversity and deliver ecosystem services. Understanding the components underlying this complexity can aid the development of effective strategies for ecosystem conservation. Caribbean coral reefs support and protect millions of livelihoods, but recent anthropogenic change is shifting communities toward reefs dominated by stress-resistant coral species, which are often less architecturally complex. With the regionwide decline in reef fish abundance, it is becoming increasingly important to understand changes in coral reef community structure and function. We quantify the influence of coral composition, diversity, and morpho-functional traits on the architectural complexity of reefs across 91 sites at Cozumel, Mexico. Although reef architectural complexity increases with coral cover and species richness, it is highest on sites that are low in taxonomic evenness and dominated by morpho-functionally important, reef-building coral genera, particularly Montastraea. Sites with similar coral community composition also tend to occur on reefs with very similar architectural complexity, suggesting that reef structure tends to be determined by the same key species across sites. Our findings provide support for prioritizing and protecting particular reef types, especially those dominated by key reef-building corals, in order to enhance reef complexity.     

Natural and anthropogenic influences on the diversity structure of reef fish communities in the Tuamotu Archipelago (French Polynesia)

Despite the rapid rate of human-induced species losses, the relative influence of natural and anthropogenic factors on the functional diversity of species assemblages remains unknown for most ecosystems. A model was previously developed to predict the diversity structure of coral reef fish assemblages in 10 atolls of low human pressure and contrasting morphology of the Tuamotu Archipelago (French Polynesia). This existing model predicted smoothed histograms (spectra) of species richness according to size classes, diet classes and life-history classes of fish assemblages using a combination of environmental characteristics at different spatial scales. The present study applied the model to Tikehau, another atoll of the same archipelago where commercial fishing is practiced and where the same sampling strategy was reproduced. Significant differences appeared between predicted and observed species richness in several size, diet and life-history classes of fish assemblages in Tikehau. Two parameters which were not accounted for in the initial model, i.e. fishing pressure and atoll position within the archipelago, explained together 63% of variance in model residuals, >60% being explained by fishing pressure only. The respective effects of fishing and atoll position on the diversity of coral reef fish assemblages are discussed, with the potential of such modelling approach to assess the relative importance of factors affecting functional diversity within communities.     

Spatial cost–benefit analysis of blue restoration and factors driving net benefits globally

Marine coastal ecosystems, commonly referred to as blue ecosystems, provide valuable services to society but are under increasing threat worldwide due to a variety of drivers, including eutrophication, development, land-use change, land reclamation, and climate change. Ecological restoration is sometimes necessary to facilitate recovery in coastal ecosystems. Blue restoration (i.e., in marine coastal systems) is a developing field, and projects to date have been small scale and expensive, leading to the perception that restoration may not be economically viable. We conducted a global cost–benefit analysis to determine the net benefits of restoring coral reef, mangrove, saltmarsh, and seagrass ecosystems, where the benefit is defined as the monetary value of ecosystem services. We estimated costs from published restoration case studies and used an adjusted-value-transfer method to assign benefit values to these case studies. Benefit values were estimated as the monetary value provided by ecosystem services of the restored habitats. Benefits outweighed costs (i.e., there were positive net benefits) for restoration of all blue ecosystems. Mean benefit:cost ratios for ecosystem restoration were eight to 10 times higher than prior studies of coral reef and seagrass restoration, most likely due to the more recent lower cost estimates we used. Among ecosystems, saltmarsh had the greatest net benefits followed by mangrove; coral reef and seagrass ecosystems had lower net benefits. In general, restoration in nations with middle incomes had higher (eight times higher in coral reefs and 40 times higher in mangroves) net benefits than those with high incomes. Within an ecosystem type, net benefit varied with restoration technique (coral reef and saltmarsh), ecosystem service produced (mangrove and saltmarsh), and project duration (seagrass). These results challenge the perceptions of the low economic viability of blue restoration and should encourage further targeted investment in this field.     

Examining the relationship between ecosystem structure and function using structural equation modelling: A case study examining denitrification potential in restored wetland soils

An ongoing debate in ecology is the relationship between community or ecosystem structure and function. This relationship is particularly important in restored ecosystems because it is often assumed that restoring ecosystem structure will restore ecosystem functioning, but this assumption is frequently not tested. In this study, we used a novel application of structural equation modelling (SEM) to examine the relationship between ecosystem structure and function. To exemplify how to apply SEM to explore this relationship, we used a case study examining soil controls on denitrification potential (DNP) in two restored wetlands. Our objectives were to examine (1) whether both restored wetland soil ecosystems had similar relationships among soils variables (i.e. similar soil ecosystem structure) and (2) whether the soil variables driving denitrification potential (DNP) were similar at both sites (i.e. the soil ecosystems were functioning in a similar manner). Using the unique ability of SEM to test model structure, we proposed a SEM to represent the soil ecosystem and tested this structure with field data. We determined that the same model structure was supported by data from both systems suggesting that the two restored wetland systems had similar soil ecosystem structure. To test whether both ecosystems were functioning in a similar way, we examined the parameters of each model. We determined that the drivers of DNP function were not the same at both sites. Higher soil organic matter was the most important predictor of higher DNP at both sites. However, the other significant relationships among soils variables were different at each system indicating that the soils were not functioning in exactly the same way at each site. Overall, these results suggest that the restoration of ecosystem structure may not necessarily ensure the restoration of ecosystem functioning. In this study we capitalize on an inherent feature of SEM, the ability to test model structure, to test a fundamental ecological question. This novel approach is widely applicable to other systems and improves our understanding of the general relationship between ecosystem structure and function.     

A tree and climate assessment tool for modelling ecosystem response to climate change

Understanding how vulnerable forest ecosystems are to climate change is a key requirement if sustainable forest management is to be achieved. Modelling the response of species in their regeneration niche to phenological and biophysical processes that are directly influenced by climate is one method for achieving this understanding. A model was developed to investigate species resilience and vulnerability to climate change within its fundamental-regeneration niche. The utility of the developed model, tree and climate assessment (TACA), was tested within the interior Douglas-fir ecosystem in south-central British Columbia. TACA modelled the current potential tree species composition of the ecosystem with high accuracy and modelled significant responses amongst tree species to climate change. The response of individual species suggests that the studied ecosystem could transition to a new ecosystem over the next 100 years. TACA showed that it can be an effective tool for identifying species resilience and vulnerability to changes in climate within the most sensitive stage of development, the regeneration phase. The TACA model was able to identify the degree of change in phenological and biophysical variables that control tree establishment, growth and persistence. The response to changes in one or more of these variables resulted in changes in the climatic suitability of the ecosystem for species and enabled a measure of vulnerability to be quantified. TACA could be useful to forest managers as a decision support tool for adaptation actions and by researchers interested in modelling stand dynamics under climate change.     

Motile cryptofauna associated with live and dead coral substrates: implications for coral mortality and framework erosion

Coral reef cryptofauna are a diverse group of metazoan taxa that live within intra- and inter-skeletal voids formed by framework structures. Despite a hypothesized high biomass and numerous trophic roles, they remain uncharacterized relative to exposed reef communities. Motile cryptofauna were sampled from live coral colonies and dead frameworks typifying four successive levels of degradation on an eastern Pacific pocilloporid reef. Abundances and biomass were higher on live versus dead corals habitats. The density of cryptofauna per volume substrate was highest on dead coral frameworks of intermediate degradation, where complex eroded substrates provide abundant shelters. These data have important and far-reaching ramifications for how the diverse multispecies assemblages that are reef ecosystems will respond to anthropogenic stressors such as those associated with climate change. Extreme levels of coral mortality, bioerosion, and habitat destruction will lead to impairment and eventually loss of ecosystem functions.     

Positive and Negative Effects of a Threatened Parrotfish on Reef Ecosystems

Species that are strong interactors play disproportionately important roles in the dynamics of natural ecosystems. It has been proposed that their presence is necessary for positively shaping the structure and functioning of ecosystems. We evaluated this hypothesis using the case of the world's largest parrotfish (Bolbometopon muricatum), a globally imperiled species. We used direct observation, animal tracking, and computer simulations to examine the diverse routes through which B. muricatum affects the diversity, dispersal, relative abundance, and survival of the corals that comprise the foundation of reef ecosystems. Our results suggest that this species can influence reef building corals in both positive and negative ways. Field observation and simulation outputs indicated that B. muricatum reduced the abundance of macroalgae that can outcompete corals, but they also feed directly on corals, decreasing coral abundance, diversity, and colony size. B. muricatum appeared to facilitate coral advancement by mechanically dispersing coral fragments and opening up bare space for coral settlement, but they also damaged adult corals and remobilized a large volume of potentially stressful carbonate sediment. The impacts this species has on reefs appears to be regulated in part by its abundance—the effects of B. muricatum were more intense in simulation scenarios populated with high densities of these fish. Observations conducted in regions with high and low predator (e.g., sharks) abundance generated results that are consistent with the hypothesis that these predators of B. muricatum may play a role in governing their abundance; thus, predation may modulate the intensity of the effects they have on reef dynamics. Overall our results illustrate that functionally unique and threatened species may not have universally positive impacts on ecosystems and that it may be necessary for environmental managers to consider the diverse effects of such species and the forces that mediate the strength of their influence. Efectos Positivos y Negativos de un Pez Loro Amenazado Sobre Ecosistemas Arrecifales     

Landsat Thematic Mapper: Detection of Shifts in Community Composition of Coral Reefs

Abstract: We assembled a time series of 20 Landsat thematic mapper images from 1982 to 1996 for Key Largo, Florida, to ascertain whether satellite imagery can detect temporal changes in coral reef communities. Selected reef and control areas were examined for changes in brightness, spectral reflectance, band ratios, spatial texture, and temporal texture (  pixel-to-pixel change over time). We compared the data to known changes in the reef ecosystem of Carysfort Reef and terrestrial sample sites. Changes in image brightness and spectral-band ratios were suggestive of shifts from coral- to algal-dominated community structure, but the trends were not statistically significant. The spatial heterogeneity of the reef community decreased in the early 1980s at scales consistent with known ecological changes to the coral community on Carysfort Reef. An analysis of pixel-scale variation through time, termed temporal texture, revealed that the shallow reef areas are the most variable in regions of the reef that have experienced significant ecological decline. Thus, the process of reef degradation, which alters both the spatial patterning and variability of pixel brightness, can be identified in unclassified thematic mapper images.     

EcoTroph: Modelling marine ecosystem functioning and impact of fishing

EcoTroph (ET) is a model articulated around the idea that the functioning of aquatic ecosystems may be viewed as a biomass flow moving from lower to higher trophic levels, due to predation and ontogenetic processes. Thus, we show that the ecosystem biomass present at a given trophic level may be estimated from two simple equations, one describing biomass flow, the other their kinetics (which quantifies the velocity of biomass transfers towards top predators). The flow kinetic of prey partly depends on the abundance of their predators, and a top-down equation expressing this is included in the model. Based on these relationships, we simulated the impact on a virtual ecosystem of various exploitation patterns. Specifically, we show that the EcoTroph approach is able to mimic the effects of increased fishing effort on ecosystem biomass expected from theory. Particularly, the model exhibits complex patterns observed in field data, notably cascading effects and ‘fishing down the food web’. EcoTroph also provides diagnostic tools for examining the relationships between catch and fishing effort at the ecosystem scale and the effects of strong top-down controls and fast-flow kinetics on ecosystems resilience. Finally, a dynamic version of the model is derived from the steady-state version, thus allowing simulations of time series of ecosystem biomass and catches. Using this dynamic model, we explore the propagation of environmental variability in the food web, and illustrated how exploitation can induce a decrease of ecosystem stability. The potential for applying EcoTroph to specific ecosystems, based on field data, and similarities between EcoTroph and Ecopath with Ecosim (EwE) are finally discussed.     

A numerical model of wave- and current-driven nutrient uptake by coral reef communities

We developed a numerical model capable of simulating the spatial zonation of nutrient uptake in coral reef systems driven by hydrodynamic forcing (both from waves and currents). Relationships between nutrient uptake and bed stress derived from flume and field studies were added to a four-component biogeochemical model embedded within a three-dimensional (3-D) hydrodynamic ocean model coupled to a numerical wave model. The performance of the resulting coupled physical-biogeochemical model was first evaluated in an idealized one-dimensional (1-D) channel for both a pure current and a combined wave-current flow. Waves in the channel were represented by an oscillatory flow with constant amplitude and frequency. The simulated nutrient concentrations were in good agreement with the analytical solution for nutrient depletion along a uniform channel, as well as with existing observations of phosphate uptake across a real reef flat. We then applied this integrated model to investigate more complex two-dimensional (2-D) nutrient dynamics, firstly to an idealized coral reef-lagoon morphology, and secondly to a realistic section of Ningaloo Reef in Western Australia, where nutrients were advected into the domain via alongshore coastal currents. Both the idealized reef and Ningaloo Reef simulations showed similar patterns of maximum uptake rates on the shallow forereef and reef crest, and with nutrient concentration decreasing as water flowed over the reef flat. As a result of the cumulative outflow of nutrient-depleted water exiting the reef channels and then being advected down the coast by alongshore currents, both reef simulations exhibited substantial alongshore variation in nutrient concentrations. The coupled models successfully reproduced the observed spatial-variability in nitrate concentration across the Ningaloo Reef system.