Hydrology and water quality are innately linked, as flow dynamics control the transport of pollutants within river systems. Consequently, the timing of sample collection in water quality monitoring programs strongly influences the accuracy of estimated pollutant loads. To minimise error, concentrations should be sampled across the hydrograph, capturing the rising limb, peak, and falling limb, to reflect the dynamic nature of pollutant transport. However, in river systems with variable flow regimes, predicting the timing and duration of events is challenging. Monitoring programs often resort to oversampling to ensure that critical periods are represented, but this approach increases effort and cost. In this study, we apply probabilistic gradient boosting decision tree regression (CatBoost) to forecast river height in a tropical, fast-response catchment characterised by high-flow variability, using hourly rainfall, discharge, and river height data collected over a 15-year period. Model performance was evaluated across forecast horizons ranging from 1 to 48 h. The models reproduced hydrograph magnitude, shape, and timing with high accuracy at short horizons (1–12 h), while forecast confidence and accuracy declined progressively at longer horizons (24–48 h). Forecast performance also varied across flow regimes: low flows were predicted accurately across all horizons, moderate flows reliably up to the 24-h horizon, and high flows up to the 12-h horizon. Predictive skill declined for extreme events; however, forecasts remained operationally valuable up to the 12-h horizon. These findings highlight the potential for short-term forecasts to support adaptive, resource-efficient sampling programs and reduce reliance on oversampling while maintaining pollutant load accuracy.

This manuscript describes the collation of available water quality data from the freshwater reaches of surface streams within the Great Barrier Reef catchment area, northeastern Australia. This compilation represents one of the most comprehensive online datasets for historical tropical and subtropical freshwater quality around the world. We document the criteria for selection of the data and associated publications as well as the processes of data cleaning used to produce a qualitative assessment of the datasets. The final compilation includes 41 individual datasets that collectively report 466 sites and contain over 26,000 discrete water quality sample records totaling more than 350,000 unique water quality results. Finally, we outline the nuances of the data that end users need to take into account when combining them for spatial and temporal analyses. The dataset ensures that these valuable water quality data collected over the past four decades are preserved for the next generations of researchers, practitioners, management agencies and policy makers.

Water clarity on the inshore Great Barrier Reef (GBR) is greatly influenced by terrestrial runoff of suspended particulate matter (SPM). Catchment sediment tracing studies often do not extend into the marine environment, preventing the analysis of preferential marine transport. This study employs novel collection and sediment tracing techniques to examine the transport of the terrigenous 'mineral' component of plume SPM within the GBR lagoon for two flood events. Utilising geochemical, radionuclide and clay mineral analysis, we trace terrigenous mineral sediments > 100 km from the river mouth. We show that the SPM geochemistry is highly influenced by particle-size fractionation, desorption, and dilution within the plume, rendering traditional tracing methods unviable. However, the ratios of rare earth elements (REE) to thorium (Th) provide stable tracers of mineral SPM transported across the catchment to marine continuum and allow the identification of discrete catchment sources for each flood event. Plume sediment radionuclides are also stable and consistent with sub-surface erosion sources.

Increased delivery of sediment and nutrients from the land threatens the health and productivity of key ecosystems of the Great Barrier Reef (GBR) lagoon. This chapter is an update to the Furnas and Mitchell (2000) "Runoff of terrestrial sediment and nutrients into the Great Barrier Reef World Heritage Area" chapter from the first edition and incorporates our latest understanding of GBR catchment sediment and nutrient generation processes, transport, and transformations. We provide a review of the history of monitoring and research in the GBR Catchment Area (GBRCA) that has led to improved estimates of sediment and nutrient loads and how it has changed over time under catchment development. This includes targeted monitoring, tracing, and modelling approaches and proxy-based evidence within both the catchment and lagoon. This review emphasises the increasing use of the latest high temporal frequency, near real time sensor technologies to capture the complexity of hydrology, sediment, and nutrient runoff at small-scale tributary sites, including the highly elevated concentrations associated with the first-flush runoff. We present the latest 'best available' load estimates from each of the 35 basins of the GBRCA for fine sediment (< 20 µm fraction), particulate nitrogen and phosphorus, and dissolved inorganic nitrogen. Finally, we consider the available management options to reduce the loads of sediment and nutrients delivered to the GBR lagoon that include policy instruments.

River run-off has long been regarded as the largest source of organic-rich suspended particulate matter (SPM) in the Great Barrier Reef (GBR), contributing to high turbidity, pollutant exposure and increasing vulnerability of coral reef to climate change. However, the terrestrial versus marine origin of the SPM in the GBR is uncertain. Here we provide multiple lines of evidence ( 13 C NMR, isotopic and genetic fingerprints) to unravel that a considerable proportion of the terrestrially-derived SPM is degraded in the riverine and estuarine mixing zones before it is transported further offshore. The fingerprints of SPM in the marine environment were completely different from those of terrestrial origin but more consistent with that formed by marine phytoplankton. This result indicates that the SPM in the GBR may not have terrestrial origin but produced locally in the marine environment, which has significant implications on developing better-targeted management practices for improving water quality in the GBR.

Excess fine sediment delivery is a major contributor to the declining health of the Great Barrier Reef and identifying the dominant source areas of fine sediment has been critical to prioritising erosion remediation programs. The Bowen River catchment within the Burdekin Basin has been recognised as a major contributor and hence received considerable research investment over the last two decades. This study adopts a novel approach to integrate three independently derived sediment budgets produced from a catchment scale sediment budget model (Dynamic SedNet), targeted tributary water quality monitoring and geochemical sediment source tracing to refine and map the sediment source zones within the Bowen catchment. A four year study of water quality monitoring combined with modelled discharge estimates and geochemical source tracing both identified that the Little Bowen River and Rosella Creek were the largest sources of sediment in the Bowen River catchment. Both data sets contradicted initial synoptic sediment budget model predictions due to inadequate representation of hillslope and gully erosion. Recent improvements in model inputs have resulted in predictions that are consistent with the field data and are of finer resolution within the identified source areas. Priorities for further investigation of erosion processes are also revealed. Examining the benefits and limitations of each method indicates that these are complimentary methods which can effectively be used as multiple lines of evidence. An integrated dataset such as this provides a higher level of certainty in the prediction of fine sediment sources than a single line of evidence dataset or model. The use of high quality, integrated datasets to inform catchment management prioritisation will provide greater confidence for decision makers when investing in catchment management.

Sediments collected within freshwater, estuarine and marine habitats were used to trial various chemical and physical pre-treatments to develop a systematic protocol for grain-size analysis using laser diffraction. Application of this protocol mitigates the influence of bio-physical processes that may transform grain-size distributions, enabling the characterisation and quantification of 'primary' mineral sediments across the complex freshwater-marine continuum to be more reliably assessed. Application of the protocol to two Great Barrier Reef (Australia) river catchments and their estuaries reveals the ecologically relevant <20 μm fraction comprises a larger component of exported sediment than existing methods indicate. These findings are highly relevant when comparing measured data to grain-size-specific modelled sediment loads and water-quality targets. Finally, adoption of the protocol also improves the environmental interpretation of the influence of 'terrigenous sediment' in marine settings, including quantification of newly-delivered flood plume sediment.

Variation in water quality can directly affect the composition of benthic assemblages on coral reefs. Yet, few studies have directly quantified nutrient and suspended particulate matter (SPM) to examine their potential impacts on benthic community structure, especially around high oceanic islands. We assessed the spatiotemporal variation of nutrients and SPM across six sites in American Samoa over a 12-month period and used exploratory path analysis to relate dissolved inorganic nutrients, land use, and natural and anthropogenic drivers to benthic assemblages on adjacent shallow reefs. Multivariate analyses showed clear gradients in nutrient concentrations, sediment accumulation and composition, and benthic structure across watersheds. Instream nutrients and land uses positively influenced reef flat nutrient concentrations, while benthic assemblages were best predicted by wave exposure, runoff, stream phosphate and dissolved inorganic nitrogen loads. Identifying locality-specific drivers of water quality and benthic condition can support targeted management in American Samoa and in other high islands.

This study quantified the bioavailable nitrogen contribution from riverine plumes to Great Barrier Reef (GBR) coastal environments. The potential bioavailable nitrogen from two Dry Tropics riverine plumes was considerable [9 -30% added to the end-of-catchment dissolved inorganic nitrogen (DIN) load]. Particulate inorganic nitrogen conversion to DIN was an important process in short timeframes (25% to 100% of the generated load). The remaining load was contributed by microbial mineralisation of organic nitrogen. Flood plume sediment has potential to generate nitrogen once deposited and/or resuspended. Nitrogen generation was insignificant in a few plumes where immobilisation of nitrogen in bacteria biomass occurred. The source of organic matter in the plumes and availability of nitrogen relative to organic matter were important determinants of mineralisation/ immobilisation. This research demonstrates that riverine plumes have potential to be considerable sources of bioavailable nitrogen to coastal environments of the GBR and that organic matter is a key bioavailability driver.

Catchment impacts on downstream ecosystems are difficult to quantify, but important for setting management targets. Here we compared 12 years of monitoring data of seagrass area and biomass in Cleveland Bay, northeast Australia, with discharge and associated sediment loads from nearby rivers. Seagrass biomass and area exhibited different trajectories in response to river inputs. River discharge was a slightly better predictor of seagrass indicators than total suspended solid (TSS) loads, indicating that catchment effects on seagrass are not restricted to sediment. Linear relationships between Burdekin River TSS loads delivered over 1-4 years and seagrass condition in Cleveland Bay generated Ecologically Relevant Targets (ERT) for catchment sediment inputs. Our predicted ERTs were comparable to those previously estimated using mechanistic models. This study highlights the challenges of linking catchment inputs to condition of downstream ecosystems, and the importance of integrating a variety of metrics and approaches to increase confidence in ERTs.

The novel application of the SediPump® sampling device to capture sufficient sediment mass from low concentration flood plume waters has enabled catchment source tracing of GBR flood plume sediment for the first time. Focused on the single largest exporter of sediment to the GBR, the Burdekin River, three wet season discharge events were sampled from 2017 to 2019 to characterise and trace flood plume suspended sediments using geochemistry, fallout radionuclides and clay mineralogy. Sampling targeted the end-of-river (EoR) flow hydrograph to capture contributing catchment sources, and flood plume samples from both the adjacent turbid primary waters and offshore secondary waters up to 160 km from the EoR. Analysis of EoR and plume sediment major element geochemistry indicates standard geochemical sediment tracing approaches cannot be applied to a large river catchment such as this, or across the catchment-marine continuum, where particle fractionation has occurred both within the catchment and across the salinity gradient from the river mouth. Further, the secondary plume sediments have also been affected by the addition of marine-sourced carbonate and biogenic silica. We show elemental ratios of the rare earth elements (REE) and thorium (Th) can be used as stable tracers across this continuum, and importantly, used to trace Burdekin plume terrigenous sediment transported >100 km’s from the river mouth back to its EoR REE/Th signal, which was unique for each of the three discharge events. These ratios were also used to trace this sediment to a major sub-catchment source. Additional fallout radionuclide 137Cs analysis of a sub-set of Burdekin EoR and plume samples also reveal sediment being transported in these GBR flood plumes are almost exclusively derived from sub-surface erosion processes.

Land use in the catchments draining to the Great Barrier Reef lagoon has changed considerably since the introduction of livestock grazing, various crops, mining and urban development. Together these changes have resulted in increased pollutant loads and impaired coastal water quality. This study compiled records to produce annual time-series since 1860 of human population, livestock numbers and agricultural areas at the scale of surface drainage river basins, natural resource management regions and the whole Great Barrier Reef catchment area. Cattle and several crops have experienced progressive expansion interspersed by declines associated with droughts and diseases. Land uses which have experienced all time maxima since the year 2000 include cattle numbers and the areas of sugar cane, bananas and cotton. A Burdekin Basin case study shows that sediment loads initially increased with the introduction of livestock and mining, remained elevated with agricultural development, and declined slightly with the Burdekin Falls Dam construction.

Catchment activities, such as logging, grazing, agriculture and urbanization,generate elevated sediment loads which impact downstream water quality and coastal ecosystems. Quantifying the complex link between catchment sediment sources and downstream ecosystems is challenging but important for the development of reliable land-based ecologically relevant load targets. With this goal in mind, we compared condition of seagrass (area and biomass) in Cleveland Bay, northeast Australia, to river discharge and associated sediment loads, fitting linear models to 12 years of routine monitoring data. The data demonstrate that the Burdekin catchment dominates sediment delivery to Cleveland Bay. Annual changes in the area and biomass of shallow subtidal seagrass were significantly correlated with annual total suspended solid (TSS) loads from the Burdekin River (and to flow, in the case of area). However annual TSS loads were not good predictors of change in area and biomass across all seagrass communities. Neither area nor biomass was significantly correlated to annual sediment (i.e. TSS and fine sediment) loads for both the shallow subtidal community, and all communities combined, but area was significantly correlated to 4-year antecedent TSS and fine sediment loads. The results demonstrate that the trajectory of decline and recovery differed between biomass and area, and suggest that processes occurring on annual timescales drive year-to-year variation, but that seagrass state is affected by conditions accumulating over longer time periods. The findings also highlight different responses of subtidal and intertidal seagrasses to TSS loads. Fine sediment (particle size 0.55, p<0.01) were used to estimate “sediment load thresholds”, above which seagrass was predicted to decline or fail to meet desired state. These threshold loads were equivalent to a reduction of the anthropogenic fine sediment load in the Burdekin River by 38-49%. Allowing for uncertainty, our estimate of sediment load reductions is comparable to those in the WQIP 2018. Achieving these load reductions would not guarantee that seagrass in Cleveland Bay achieves the desired state, but similarity between estimates generated from independent approaches strengthens confidence in these targets, while highlighting the challenges in quantifying the effect of terrestrial activities on downstream ecosystems. Flow was a better predictor of seagrass than TSS load, indicating that catchment inputs on seagrass are not restricted to sediment loads and reflecting the fact that events linked to high discharge can independently impact seagrass state (e.g. direct damage or sediment resuspension associated with storms or cyclones). The interaction of natural and anthropogenic processes over a large range of spatial and temporal scales makes it hard to assign causality in systems such as these, but since catchments do clearly impact ecosystems downstream, efforts to quantify these connections are important, to protect ecosystems and their capacity to deliver ecosystem services.

Catchment degradation causing increased sediment flow is one of the key stressors facing Great Barrier Reef (GBR) habitats.Ecologically relevant targets (ERTs) for sediment and nutrient loads have been previously proposed based on seagrass light requirements, the next step is to connect these to ecological response.The overarching goal of the present work is to recommend preliminary thresholds that can be used in the development of more refined ERTs.To achieve this, we perform statistical analysis on datasets for catchment flows and sediment loads and condition of the adjacent seagrass habitat, to identify what might be the direct impacts of catchment discharge on seagrass and the associated timescales of ecological response.Our case study focuses on Cleveland Bay, which is located in the central GBR, and has important seagrass habitat that is affected by discharge from the Burdekin River.Annual monitoring of seagrass biomass and area has been undertaken since 2007.We compare these ecological time-series with data for Burdekin River annual flow and total sediment load from 2005 onwards.Annual Burdekin River flow varied by nearly 40-fold within the 2005-2018 study period, and declines in biomass and area of both subtidal and intertidal seagrasses were associated with high flows and loads from the Burdekin.Subtidal seagrasses appeared more sensitive to changes in catchment discharges than intertidal seagrasses, exhibiting a 3 year timeframe for recovery, following high annual flows and loads.Based on our results, a linear model relating change in seagrass biomass to Burdekin River metrics was used to calculate predicted thresholds below which seagrass biomass was likely to increase, and above which biomass was likely to decline.For seagrass area, a growth threshold, below which seagrass area expanded; and a decline threshold, above which seagrass area fell, were defined for annual Burdekin River flow, and sediment load.Overall these thresholds provide the first steps towards refining ERTs based on ecological condition, which can directly inform the management of the GBR to protect its iconic seagrass habitats and associated communities.The next step is to examine whether the relationship between river discharge and sediment load was the primary cause of seagrass decline.

Studies documenting the effects of land-derived suspended particulate matter (SPM, i.e., particulate organic matter and mineral sediment) on marine ecosystems are typically disconnected from terrestrial studies that determine their origin, transport and fate. This study reviews sources, transport, transformations, fate and effects of SPM along the ‘ridge-to-reef’ continuum. We show that some of the SPM can be transported over long distances and transformed into large and easily resuspendible organic-rich sediment flocs. These flocs may lead to prolonged reductions in water clarity, impacting upon coral reef, seagrass and fish communities. Using the Great Barrier Reef (NE Australia) as a case study, we identify the latest research tools to determine thresholds of SPM exposure, allowing for an improved appreciation of marine risk. These tools are used to determine ecologically-relevant end-of-basin load targets and reliable marine water quality guidelines, thereby enabling enhanced prioritisation and management of SPM export from ridge-to-reef.

Modelling and monitoring pollutants entering into the Great Barrier Reef (GBR) lagoon remain important priorities for the Australian and Queensland governments. Uncertainty analysis of pollutant load delivery to the GBR would: (1) inform decision makers on their ability to meet environmental targets; (2) identify whether additional measurements are required to make confident decisions; and (3) determine whether investments into remediation activities are actually making a difference to water quality and the health of the GBR. Using a case study from the Upper Burdekin catchment where sediment concentrations are the focus, herein we explore and demonstrate different ways of communicating uncertainty to a decision maker. In particular, we show how exceedance probabilities can identify hot spots for future monitoring or remediation activities and how they can be used to inform target setting activities. We provide recommendations for water quality specialists that allow them to make more informed and scientifically defensible decisions that consider uncertainty in both the monitoring and modelling data, as well as allowing the calculation of exceedances from a threshold.

Optically active water quality components (OAC) transported by flood plumes to nearshore marine environments affect light levels. The definition of minimum OAC concentrations that must be maintained to sustain sufficient light levels for conservation of light-dependant coastal ecosystems exposed to flood waters is necessary to guide management actions in adjacent catchments. In this study, a framework for defining OAC target concentrations using empirical light attenuation models is proposed and applied to the Wet Tropics region of the Great Barrier Reef (GBR) (Queensland, Australia). This framework comprises several steps: (i) light attenuation (Kd(PAR)) profiles and OAC measurements, including coloured dissolved organic matter (CDOM), chlorophyll-a (Chl-a) and suspended particulate matter (SPM) concentrations collected in flood waters; (ii) empirical light attenuation models used to define the contribution of CDOM, Chl-a and SPM to the light attenuation, and; (iii) translation of empirical models into manageable OAC target concentrations specific for wet season conditions. Results showed that (i) Kd(PAR) variability in the Wet Tropics flood waters is driven primarily by SPM and CDOM, with a lower contribution from Chl-a (r2 = 0.5, p < 0.01), (ii) the relative contributions of each OAC varies across the different water bodies existing along flood waters and strongest Kd(PAR) predictions were achieved when the in-situ data were clustered into water bodies with similar satellite-derived colour characteristics ('brownish flood waters', r2 = 0.8, p < 0.01, 'greenish flood waters', r2 = 0.5, p < 0.01), and (iii) that Kd(PAR) simulations are sensitive to the angular distribution of the light field in the clearest flood water bodies. Empirical models developed were used to translate regional light guidelines (established for the GBR) into manageable OAC target concentrations. Preliminary results suggested that a 90th percentile SPM concentration of 11.4 mg L-1 should be maintained during the wet season to sustain favourable light levels for Wet Tropics coral reefs and seagrass ecosystems exposed to 'brownish' flood waters. Additional data will be collected to validate the light attenuation models and the wet season target concentration which in future will be incorporated into wider catchment modelling efforts to improve coastal water quality in the Wet Tropics and the GBR. (C) 2018 Elsevier Ltd. All rights reserved.

Coral trace element proxies of terrestrial runoff are widely applied to document and quantify historical changes in river discharge, constituent loads and land disturbance. However, some studies show poor replication between trace element records where cores from multiple coral colonies have been analyzed. Conflicting interpretations also exist on the environmental variable the coral trace element proxy is recording. Indeed, few studies have examined trace element behavior in the estuarine mixing zone that influence the coral records and only limited data on river discharge and constituent loads are available to validate the proxy records of terrestrial runoff. This study examined the behavior of Barium (Ba), Manganese (Mn) and Yttrium (Y) in the Burdekin River estuarine mixing zone, north-eastern Australia during several flood events and investigated the ability of coral Ba/Ca, Mn/Ca and Y/Ca ratios to record the variability of measured Burdekin River discharge and suspended sediment loads along a transect of replicate coral cores (10 cores from 5 locations). The results show limited evidence for Ba desorption from suspended sediments in the estuarine mixing zone while considerable desorption of Mn over a wide salinity mixing gradient was evident. Y showed evidence of removal in the initial mixing zone of the estuary (0–5 PSU) but displayed a relatively flat pattern thereafter indicating that it was not diluted by seawater mixing. The coral trace element records generally showed poor agreement within sites and the Ba/Ca ratios in some corals did not respond to regional river discharge, although coral luminescent lines were present in all cores and were significantly correlated with each other and Burdekin River discharge. While it was difficult to disentangle the influence of Burdekin River discharge and suspended sediment loads on the coral Ba/Ca proxy, several lines of evidence point towards discharge as the major contributor to this proxy in this region. A combination of factors likely influence the coral Ba/Ca ratio including an as yet undetermined physiological mechanism possibly related to crystallography or species, distance of the coral to the river mouth, variability in river discharge (including both annual totals and peaks, and local influences), variability in sediment load, the behavior of trace elements in the estuarine mixing zone, the hydrodynamics of flood plumes in the marine environment and the water depth of the coral. While the coral Mn/Ca and Y/Ca ratios did not respond to Burdekin River discharge events, the considerable desorption of Mn and the elevated Y throughout the estuarine mixing zone shows some promise in their ability to record long-term changes in suspended sediment loading and large terrestrial disturbances. Future studies examining coral records of terrestrial runoff should examine trace element behavior in the river estuarine mixing zone of influence, establish a correlation between the trace element and river discharge (such as luminescent lines) and demonstrate replication between different coral colonies.