This dataset comprises of microbial metagenomics sequencing reads of seawater collected across 48 reef sites across the Great Barrier Reef. Samples were collected across four Long Term Monitoring Program (LTMP) field trips between November 2019-July 2020, combining water chemistry data, LTMP field surveys and microbial metagenomics data. This data collection was a major part of the QRCIF IMOS GBR microbial genomic database project, which aims to generate a comprehensive open access repositor of microbial genomic data from across the region. Seawater was collected in quadruplicate either by SCUBA or using Niskin Bottles at each reef site, 5L of seawater was pre-filtered using a 5µm filter and applied to a 0.22µm sterivex filter, snap frozen and stored at -20°C in preparation of DNA extraction. DNA was extracted from sterivex filters using phenol:chloroform:Iso-amyl alcolol extraction, ethanol precipitation and cleanup using the Zymo Clean and Concentrator® kit before submission for sequencing at the Australian Centre for Ecogenomics sequencing facility, Illumina. The data presented as illumina paired-end shotgun metagenomics sequencing runs, in fastq format, generated by Microba Life Sciences, Brisbane, QLD, Australia. Each downloadable archive contains forward and reverse reads for all replicate sampling performed at that particular site. Water quality particulate and dissolved nutrient data was generated as previously described (https://doi.org/10.25845/5c09b551f315b) from water samples collected simultaneously at each reef site. Zip files are available through the spatial layer under each site's 'illumina.seawater.zip' - please note these are large downloads (between 6 - 14 GB).

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).

Nutrient data was obtained from the lower reaches and estuaries of 23 rivers discharging into the Great Barrier Reef lagoon. Wet season time series were measured in five rivers (South Johnstone River, Tully River, Herbert River, Burdekin River and Fitzroy River). Seven rivers have catchments in the wet tropical region (Barron River, Mulgrave River, Russell River, North Johnstone River, South Johnstone River, Tully River and Murray River). The Normanby River and Herbert River have mixed wet/dry catchments. Two major dry catchment rivers, the Burdekin River and the Fitzroy River were sampled.Sporadic samples, usually from the estuary, were collected in the course of other projects. These include Jacky Jacky Creek, Escape River, Pascoe River, Claudie River, Lockhardt River, McIvor River, Daintree River, Ross River, Alligator Creek, Haughton River, Barratta Creek and Pioneer River.In most cases, near-surface water samples were collected from mid-channel, above the level of saltwater intrusion, using a clean plastic bucket or jar lowered by rope. Prior to December 1991, only single water samples were collected at any one time; thereafter, collection of duplicate water samples was progressively introduced into all sampling programs. Sampling was undertaken to:1. quantify terrestrial input fluxes of nutrient elements (N, P, Si) which influence plankton productivity, reef productivity and water quality in the central GBR region2. resolve regional, seasonal and event-associated exports of nutrients from north Queensland rivers with both wet and dry catchments3. resolve the dynamics of river nutrient fluxes during flood events, especially large events associated with cyclones and monsoonal rain depression4. collect data suitable for parameterizing numerical flow discharge models for major north Queensland river systems Sampling was conducted through cooperative arrangements between AIMS and other government agencies. These include the Great Barrier Reef Marine Park Authority (GBRMPA), Queensland Department of Primary Industries (QDPI), Bureau of Sugar Experiment Stations (BSES), Queensland Water Resources Commission (QWRC), Cairns City Council (CCC), CSIRO and Central Queensland University (CQU). A number of volunteers also contributed to the sampling effort.

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.