The collection is a geochemical data set describing characterising the water column, porewater and sediment at various locations in the Peel-Harvey Estuary and the Murray River in Western Australia. This restricted estuary has suffered from eutrophication and algal blooms for decades in response to anthropogenic nutrient inputs. Our research is aimed at understanding the coupled cycles of carbon, iron, phosphorus and sulfur in the estuary, and their relation to eutrophication and the associated environmental issues. During three consecutive field trips in 2010, 2011 and 2012, the water column and sediment at 7 sites have been sampled. Four of these sites have been sampled more than once. The water column was sampled and analysed using a data sonde combined with collection of water samples from various depths for further analyses. Sediments were taken using a coring device, after which the sediments were sectioned into 1 - 3 cm depth intervals. Porewater was extracted by centrifugation, and the porewater and sediment residue were used for routine and advanced analyses.