This dataset details water samples collected across the flood hydrograph at the pontoon of the Fitzroy Motor Boat Club downstream of the Fitzroy River Barrage in Rockhampton. A number of samples were also collected at the Fitzroy River mouth during the 2004 floods as well as three stormwater samples from urban runoff in south Rockhampton in early January 2005. Sixteen sediment grab samples were obtained in August 2004 (survey 268, c/- Lynda Radke, Geoscience Australia). Due to project budget constraints, only nine samples (which were closest to the mouth of the river) were analysed for PAHs to obtain some idea of levels of organic contaminants in the surface sediments. Additional surface benthic sediments were obtained in August and December 2005 from the main channel of the Fitzroy River downstream of the Barrage, as well as from a few sites upstream of the Barrage. A 2.6 m sediment core (277VC20A) from Keppel Bay was obtained using a vibracorer in September 2004 (c/- Geoscience Australia); location: -23.50329°, 150.95235°. The core was sliced into 3–5 cm thick sections, in order to have adequate mass (minimum 75 g wet sediment) for the analyses of low-level PAH contaminants. Fifteen (of the 78 total) slices were analysed for PAHs, while 23 other slices were analysed for metals. Due to limited time and budget to undertake further sampling, some archived (V. Vicente-Beckett, CQU) Keppel Bay sediments (obtained in 1998), main Fitzroy Channel sediments (obtained in 2002), and a sediment core (3410) taken at the mouth of Raglan Creek in the Fitzroy Estuary (obtained by hydraulic coring from the RV Lady Basten, c/- Australian Institute of Marine Science) were included in this study in order to obtain a more extensive picture of sediment metal contents in the Fitzroy Estuary.