This research focused on defining improved water quality guideline trigger values for the GBR Water Quality Guidelines, by identifying measures of changes in coral reefs that are specifically related to recent and past exposure to changing water quality from altered catchments. An analysis of spatial and seasonal water quality conditions in six NRM regions on the GBR assessed the relationships between water quality and reef ecosystem health. Trigger values for water quality were determined to protect ecosystem health and model based predictions for ecosystem benefits for improvements should the trigger values by implemented. Analysis was conducted for the six NRM regions: Burnett Mary, Fitzroy, Mackay Whitsundays, Burdekin Dry Tropics, Wet Tropics, and Cape York NRM. This included nine water quality parameters were analysed: Secchi depth, chlorophyll, suspended solids, particulate, dissolved and total nitrogen, and particulate, dissolved and total phosphorus. Four groups of biota were used as proxies for reef ecosystem status and biodiversity: these were macroalgal cover, species richness of hard corals, and species richness of phototrophic and heterotrophic octocorals. Two separate approaches were used to define water quality guideline trigger values: (i) The modelled relationships between the condition of reef biota (ii) The analyses of the spatial distribution of water quality. The chlorophyll and nutrient data were collected since 1976, and between 1992 and 2006 as part of the Long-Term Chlorophyll Monitoring program, and of the Reef Plan Marine Monitoring program since 2005. The Secchi data were collected by a consortium of people from AIMS, DPIF, and members of the Reef Plan Marine Monitoring Program since 1976. These data are available through the data links on this page (eAtlas). The hard coral biodiversity data were collected between 1994 and 2001. The study was funded by the Great Barrier Reef Marine Park Authority, the Australian Institute of Marine Science and the Australian Government’s Marine and Tropical Sciences Research Facility

The chlorophyll monitoring under the Reef Plan Marine Monitoring Programme (Reef Plan MMP) is an extension from the Long-term Chlorophyll Monitoring Program, which was initiated by the Great Barrier Reef Marine Park Authority (GBRMPA) in December 1992 as a long-term water quality monitoring program. The chlorophyll monitoring has been managed by the Australian Institute of Marine Science since 1999 and is an important part of the AIMS water quality research and monitoring activities. Since 2005, the Chlorophyll Monitoring is a component of the Reef Plan Marine Monitoring Program, a responsibility of the GBRMPA under the Reef Water Quality Protection Plan. Sample analysis and data management has been undertaken by AIMS. The Great Barrier Reef (GBR) is the largest contiguous coral reef ecosystem in the world. The biological productivity of the GBR is supported by nutrients (e.g. nitrogen, phosphorus, silicate, iron) supplied from a number of sources, including upwelling from the Coral Sea, rainwater, nitrogen fixation by cyanobacteria and runoff from the adjacent catchment. Freshwater runoff is the largest source of new nitrogen to the GBR, however, the nutrients used by GBR marine primary producers (phytoplankton, benthic algae, seagrasses and mangroves) come predominantly from recycling of nutrients already in the system. Water quality is one of the most important factors determining the long-term health of the Great Barrier Reef (GBR). Increased nutrient availability, for example from human activity (e.g. agricultural runoff, soil erosion, discharges of sewage and aquaculture waste) usually leads to an increase in chlorophyll concentrations in coastal waters because of increased phytoplankton biomass. Phytoplankton can rapidly deplete nutrients to levels which would be difficult to sample and analyse directly. Concentrations of the plant pigment chlorophyll a (occurs in all marine phytoplankton) are a useful proxy indicator of the amount of nutrients incorporated into phytoplankton biomass. Chlorophyll a is today the most commonly used parameter for the monitoring of phytoplankton biomass and nutrient status, as an index of water quality. The data can be downloaded Data have been used for the e-Atlas: http://e-atlas.org.au/content/water-column-chlorophyll

This record describes the AIMS component of the eReefs phase 4 research program that ran from 2018 - 2020. The primary focus of eReefs phase 4 was to transition from research focused projects to operational services. The eReefs work was extended in the eReefs 2020-2024 project. eReefs is a collaboration between the Great Barrier Reef Foundation, CSIRO, the Australian Institute of Marine Science, Bureau of Meteorology, and Queensland Government. It aims to develop a platform that provides a picture of current and historical environmental conditions on the Great Barrier Reef. eReefs has many components developed and maintained by each of the organisations in the collaboration, including catchment modelling (Queensland Government), remote sensing (BOM and CSIRO), hydrodynamic modelling (BOM and CSIRO) and biogeochemical modelling (CSIRO). AIMS's contribution was providing data agregation and visualisation services and well as analysis of the biogeochemical model for inclusion in the Reef Plan report card. A major goal of the AIMS eReefs phase 4 project was to re-engineer the AIMS eReefs platform to use distributed cloud service components to make a platform that can scale its computing resources based on demand, to allow more visualisation and aggregation products to be supported in the future. The eReefs model data is very large (>15 TB) resulting high computation and storage costs associated with its processing. The new re-engineered architecture improve the computational cost efficiency by ~10x and the storage cost efficiency by 1.5x allowing a more complete set of visualisation and aggregation products to be made available. Key goals of this project were: Generating updated water quality scores based on eReefs BGC data for the Reef Plan report card based on methods developed in NESP TWQ 3.2.5. Re-engineering the AIMS eReefs platform for improved scaling. Developing a data extraction tool to allow easy access to time series data from eReefs data. The data for AIMS eReefs platform is stored on the Amazon cloud in S3 storage, managed by the AIMS Knowledge Systems team. All the data is derived from the original eReefs model data. The software was deployed on the Amazon Cloud, using AWS Batch to dynamically adjust the number of executing servers performing aggregation and animation tasks based on load. Coordination tasks are performed using AWS Lambda functions, which communicate using SNS messaging. The system coordinates the activities of all the executing tasks using a central MongoDB database. The setup of the AWS infrastructure is deployed using CloudFormation, which is a language for describing cloud computing infrastructure as code. The configuration of all the generated products (aggregation and animation) along with the infrastructure code is stored in the ereefs-definitions Git code repository. This repository has restricted access for security reasons. All other code will be made publicly available under an open source license by June 2021 as part of the eReefs 2020-2024 project. All the software for the platform is contained in 37 Git code repositories stored on GitHub. These repositories are linked to from https://github.com/open-AIMS/ereefs-documentation. This platform produces aggregation and animations of the CSIRO Hydrodynamic (GBR4 and GBR1) and BioGeoChemical eReefs models. The platform downloads model data from the National Computing Infrastructure (NCI) THREDDS data service. This data is then preprocessed to remove unused variables and half the depths, retaining only depth data from < 145m. This subsetting reduces the total storage needed by the system. This subsetted mirror is then produced to produce a range of temporal aggregations (daily, monthly, annual) and exposure products. The derived products are regridded from the original curvilinear grid used in the modelling to a regular rectangular grid. This regridding is performed to allow the data to be compatible with GIS software such as ArcMap and QGIS. All model data and derived model data is stored in NetCDF file format.

This metadata record describes physico-chemical and nutrient data collected through in situ monitoring by the Great Barrier Reef Marine Monitoring Program for Inshore Water Quality (MMP WQ). A full description of the MMP WQ and its associated datasets can be found in the parent metadata record linked above. Water quality sampling is conducted during both ambient conditions and river discharge events. Ambient monitoring refers to routine sampling during the wet and dry seasons outside of major flood events. Event-based monitoring occurs in response to major flood events to capture conditions within flood plumes; event-based monitoring occurs at the 55 routine site locations, plus 33 additional sites. The MMP WQ uses in situ sampling to measure 17 key parameters: physico-chemical: salinity, temperature, Secchi depth, total suspended solids (TSS), and coloured dissolved organic matter (CDOM); nutrient: ammonium (NH4), nitrite (NO2), nitrate (NO3), dissolved inorganic phosphorus (DIP), silicate (Si), particulate nitrogen (PN), particulate phosphorus (PP), total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), particulate organic carbon (POC), and dissolved organic carbon (DOC); and biological: chlorophyll a (Chl-a). Discrete water samples are collected with Niskin bottles at each site. Samples are collected from the surface (~0.5 m below water surface) and bottom (~1 m above the seabed) of the water column; although, for some event-based sampling only surface water samples are collected. Samples from the Niskin bottles are taken in duplicate and are analysed for the suite of water quality parameters listed above. Detailed descriptions of analytical chemistry procedures can be found in the program's annual published QA/QC report (see link below in Related Information). Brief description of collection, storage and analysis method for parameters: Salinity: 250 mL unfiltered sample, stored refrigerated at 4ºC in screw-top plastic bottle, analysed on Guildline Portasal Salinometer (temperature-compensated and calibrated using OSIL standard seawater as reference) Temperature: Electronic reversing thermometer attached to Niskin Secchi depth: The average of the vertical disappearance and reappearance depths of a Secchi disc TSS: Filtered onto pre-weighed 47 mm 0.4 µm polycarbonate membrane filter, rinsed with deionised water, dried at 60ºC for 12 hours, gravimetric analysis CDOM: 50 mL filtered sample (0.2 µm acrodisc), CDOM absorption coefficient at 443 nm calculated from absorbance measured by UV-visible absorption spectroscopy NH4, NO3, NO2 and DIP: 10 mL filtered sample (0.45 µm minisart), stored frozen at -25°C, filtrate analysed on segmented flow analyser Si: 10 mL filtered sample (0.45 µm minisart), stored refrigerated at 4ºC, filtrate analysed on segmented flow analyser (reported as Si) PN and POC: 500 mL filtered onto 25 mm GF/F, stored frozen at -25ºC, analysed by high temperature combustion (Shimadzu TOC-L) PP: 250 mL filtered onto 25 mm GF/F (0.7 µm), stored frozen at -25ºC, persulphate digestion of filter, colorific (molybdate blue) analysis on UV-Vis spectrophotometer TDN and TDP: 10 mL filtered sample (0.45 µm minisart), stored frozen at -25ºC, persulphate oxidation/digestion with mixture of NaOH, boric acid and K2S2O8 in autoclave, analysed on segmented flow analyser DOC: 10 mL filtered sample (0.45 µm minisart), acidified with 100 µL HCl, stored refrigerated at 4ºC, analysed by high temperature combustion (Shimadzu TOC-L) Chl-a: 100 mL filtered onto 25 mm GF/F (0.7 µm), stored frozen at -25ºC, extraction into 10 mL of acetone, read on Turner Fluorometer using acidification method Data can be downloaded from AIMS' main water quality database (see link below in Data Downloads). This link allows users to restrict searches to only MMP data rather than the entire database. Data are presented as depth-weighted means calculated using surface and bottom samples. Water quality data are collected in conjunction with the Great Barrier Reef Marine Monitoring Program for Inshore Coral Reefs see link below in Related Information).

The Great Barrier Reef Marine Monitoring Program for Inshore Water Quality (MMP WQ) has monitored inshore water quality of the Great Barrier Reef (GBR) lagoon since 2005 through the collection of in situ water chemistry data, along with time-series of temperature, salinity, fluorescence, and turbidity. This program is a partnership between the Great Barrier Reef Marine Park Authority, the Australian Government, the Australian Institute of Marine Science (AIMS), James Cook University (JCU), and the Cape York Water Partnership (CYWP). This metadata record also describes data from 2020-present collected by the Fitzroy Basin Marine Monitoring Program for Inshore Water Quality, which is funded by the partnership between the Australian Government’s Reef Trust and the Great Barrier Reef Foundation, and AIMS. The Paddock to Reef Integrated Monitoring, Modelling and Reporting Program (Australian and Queensland governments, 2018b) is used to evaluate the effectiveness of the implementation of the Reef 2050 Water Quality Improvement Plan (Australian and Queensland governments 2018a) and report progress towards goals and targets. The MMP WQ forms an integral part of the Paddock to Reef Program, along with other MMP components monitoring inshore coral, seagrass, and pesticides. The overarching objective of the MMP WQ is to ‘Assess temporal and spatial trends in inshore marine water quality and link pollutant concentrations to end-of-catchment loads’ (Australian and Queensland governments, 2018a). The MMP WQ is designed to measure the annual condition and long-term trends in coastal water quality. Australian tropical coastal waters are characterised by high variability in river discharge during the wet season (November - March), as rainfall from low pressure systems causes river flood plumes to extend into the coastal ocean. River discharge is generally negligible during the dry season (April - October), a period of low rainfall. 'Routine' monitoring by the MMP WQ is conducted during ambient conditions of the wet and dry seasons outside of major flood events, while 'event' monitoring occurs in response to major flood events to capture conditions within flood plumes. A summary of the Natural Resource Management (NRM) regions and associated focus regions where the MMP WQ operates is given below. The MMP WQ currently monitors a total of 55 routine sites (also sampled during events), with an additional 33 event sites monitored as required. The date ranges of routine monitoring, number of sites, and present frequency of sampling are also shown. Cape York NRM (monitored 2017-present) focus regions: Pascoe (6 sites, sampled 5 times per year) Stewart (4 sites, sampled 5 times per year) Normanby (6 sites, sampled 4 times per year) Annan-Endeavour (5 sites, sampled 5 times per year) Wet Tropics NRM (monitored 2005-present) focus regions: Barron-Daintree (6 sites, sampled 3 times per year) Russell-Mulgrave (5 sites, sampled 10 times per year) Tully (6 sites, sampled 10 times per year) Burdekin NRM (monitored 2005-present): 6 sites, sampled 9 times per year Mackay Whitsunday NRM (monitored 2005-present): 5 sites, sampled 5 times per year Fitzroy NRM (monitored 2005-2014 under MMP WQ, 2020-present under Fitzroy Basin program): 6 sites, sampled 10 times per year From 2005 to 2014, monitoring occurred 3 times per year at ~3 sites in most regions listed above. An independent statistical review of the MMP in 2014 (Kuhnert et al., 2015) showed that additional sites and higher sampling frequency would provide additional statistical power. The current program design was implemented in February 2015 and includes most of the sampling sites in the pre-2015 design, allowing for the continuation of the long-term time-series. This program re-design was reviewed and its increase in power to detect change in inshore water quality was verified (Lloyd-Jones et al., 2022). The MMP WQ uses in situ sampling to measure 17 key physico-chemical (salinity, temperature, Secchi depth, total suspended solids, and coloured dissolved organic matter), nutrient (ammonia, nitrite, nitrate, dissolved inorganic phosphorus, silicate, particulate nitrogen, particulate phosphorus, total dissolved nitrogen, total dissolved phosphorus, particulate organic carbon, and dissolved organic carbon), and biological (chlorophyll a) parameters. On every water sampling occasion, a Conductivity Temperature Depth instrument cast is done to collect a vertical profile of depth, salinity, temperature, and other water quality parameters. Data-logging instruments measuring time-series' of turbidity and fluorescence (a proxy for chlorophyll a) are deployed at 19 of the sites described above. Data-logging instruments measuring time-series' of salinity and temperature are deployed 9 of the sites described above. The details of each of these datasets are provided in the child metadata records attached to this parent record.

This dataset aggregates and summarises the water quality data collected by researchers from the Australian Institute of Marine Science from 1974 until the present. AIMS' biological oceanographers have studied the physical, chemical, and biological properties of seawater around northern Australia using a variety of methods including in situ sampling, moored sensors, and vertical profiles. This dataset contains in situ water quality information (list of analytes shown below) from northern Australia, with a large volume of data from the Great Barrier Reef, Queensland. It also contains an historical dataset transcribed from the reports of the Low Islands Expedition 1928-29 led by C.M. Yonge. This dataset contains biogeochemical data from many research expeditions (the majority led by Dr. Miles Furnas) as well as records from water quality monitoring programmes. Some data in this record were collected as part of the Great Barrier Reef Marine Monitoring Program for Inshore Water Quality (MMP WQ), which has collected in situ water quality data, along with time-series of temperature, salinity, fluorescence, and turbidity since 2005. More information about the MMP WQ can be found on its metadata record (see link below in Related Information). Each water sample occurs at a unique combination of geographic location, time, and date. In the AIMS database, samples are assigned a unique alphanumeric identifier (called a ‘station’), which is comprised of a 3-letter area code and a 3-digit station number (e.g. WQM324). Using this code, water chemistry information can be linked to other associated data, such as vertical profiles of the water column (i.e., CTD casts), which can be retrieved from AIMS’ CTD database (link below). Variables in this database include: depth, silicate (Si), ammonium (NH4), nitrite (NO2), nitrate (NO3), dissolved inorganic phosphorus (DIP), dissolved organic carbon (DOC), temperature (Temp), salinity (Sal), particulate nitrogen (PN), particulate phosphorus (PP), particulate organic carbon (POC), total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), Chlorophyll-a (Chl), phaeophytin (Phaeo), suspended solids (SS), Secchi depth, and coloured dissolved organic matter (CDOM). All analytes may not be available at every station. Brief description of collection, storage and analysis method for parameters: SAL: 250 mL unfiltered sample, stored refrigerated at 4ºC in screw-top plastic bottle, analysed on Guildline Portasal Salinometer (temperature-compensated and calibrated using OSIL standard seawater as reference) TEMP: Electronic reversing thermometer attached to Niskin SECCHI_DEPTH: The average of the vertical disappearance and reappearance depths of a Secchi disc SS: Filtered onto pre-weighed 47 mm 0.4 µm polycarbonate membrane filter, rinsed with deionised water, dried at 60ºC for 12 hours, gravimetric analysis CDOM: 50 mL filtered sample (0.2 µm acrodisc), CDOM absorption coefficient at 443 nm calculated from absorbance measured by UV-visible absorption spectroscopy NH4, NO3, NO2, and DIP: 10 mL filtered sample (0.45 µm minisart), stored frozen at -25°C, filtrate analysed on segmented flow analyser NH4_INSITU: Unfiltered 20 mL sample, processed immediately, OPA fluorescence method (post 2005) SI: 10 mL filtered sample (0.45 µm minisart), stored refrigerated at 4ºC, filtrate analysed on segmented flow analyser (reported as Si) PN_SHIM and POC: 500 mL filtered onto 25 mm GF/F, stored frozen at -25ºC, analysed by high temperature combustion (Shimadzu TOC-L) PP: 250 mL filtered onto 25 mm GF/F (0.7 µm), stored frozen at -25ºC, persulphate digestion of filter, colorific (molybdate blue) analysis on UV-Vis spectrophotometer TDN_PER and TDP_PER: 10 mL filtered sample (0.45 µm minisart), stored frozen at -25ºC, persulphate oxidation/digestion with mixture of NaOH, boric acid and K2S2O8 in autoclave, analysed on segmented flow analyser DOC: 10 mL filtered sample (0.45 µm minisart), acidified with 100 µL HCl, stored refrigerated at 4ºC, analysed by high temperature combustion (Shimadzu TOC-L) CHL and PHAEO: 100 mL filtered onto 25 mm GF/F (0.7 µm), stored frozen at -25ºC, extraction into 10 mL of acetone, read on Turner Fluorometer using acidification method Data can be downloaded from AIMS' main water quality database (see link below in Data Downloads). Data are presented as depth-weighted means calculated using surface, bottom, and any intermediate samples.