Sediment and water samples were collected using transects and grids within sampling strata, in 2019, 2020, and 2021 from a riparian reserve adjoining the Swan River estuary in Western Australia. Different sampling designs were used each year, with transects and/or grids designed to assess changes in sediment and water quality across assumed environmental gradients such as salinity or distance from possible contaminant sources. Sediments were from 0-10cm; pH and electrical conductivity were measured on suspensions, 32 elements measured by ICP-OES on HNO3/HCl digests, and microplastics counted microscopically after Fenton digestion and density separation. Surface water was from wetland ponds and stormwater drains, with pH, EC measured in-situ. Filtered acidified water subsamples used to measure nitrate + nitrite and dissolved phosphate spectrophotometrically and 26 elements using ICP-OES. Reported data include metadata and are for 231 sediment/soil samples and 172 water samples, including sampling strata categories and UTM and Longitude-Latitude coordinates. Elemental concentrations have been censored based on blank subtraction and calculated lower detection limits, with censored data presented with missing value codes.