Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region

Agricultural run-off in Australia’s Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region’s coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), alon..., This dataset comprises eDNA and chemical data obtained from water samples collected at four locations in Queensland, Australia in 2018 and again in 2020. Three of the locations are estuaries, and the fourth is the Mackay Harbour. 10 sites were selected at each estuary, at approximately 1 km intervals from the mouth of the river going upstream, and four sites were selected in the harbour. 
For chemical analyses, water samples were collected from each site following Queensland Government protocols. Samples were collected at different depths to establish a profile along the water column and measurements were averaged for each location. All samples for nutrient and pesticide analyses were placed on ice in the field and immediately refrigerated (pesticides) or frozen (nutrients) upon returning to the field laboratory until analysis. Nutrient analyses were carried out by the Chemistry Centre of the Department of Environment and Science, Queensland Government (Queensland, Australia), a NATA (N..., Microsoft Excel, Microsoft Word, Notepad, R, # Environmental DNA reveals associations between fish assemblages and seasonal changes in salinity and agricultural run-off in the Great Barrier Reef region

## Description of the data and file structure

\"Supplementary-Workbook-1_Env-Data-2018.xlsx\" and \"Supplementary-Workbook-2_Env-Data-2020.xlsx\" are Microsoft Excel workbooks for the sampled dry season (2018) and wet season (2020) respectively that contain measurements of chemical and physico-chemical parameters from the sites and locations sampled within this study. These measurements were obtained via chemical analysis of water samples from each study site.

\"Supplementary-Workbook-3_Datasets-Tele01-Elas02.xlsx\" is also an Excel workbook, containing OTU (operational taxonomic unit) tables of the occurrences of the different species detected at each sampled site in this study for two datasets - Tele01 (obtained using the Tele01 primer set) and Elas02 (obtained using the Elas02 primer set). The first tab of this spreadsheet has a k...