The use of water injection dredging (WID) is increasing in the UK's inland waterways and marinas. Jets of water are injected under low pressure directly into bottom sediment creating a turbulent water-sediment mixture that flows under the influence of gravity. Many of these sediments are highly contaminated and little is known of the effects of contaminant release on water quality or the risk to biota living in both the sediment and the water column. Sediment cores were collected from Limehouse Basin, a proposed WID site in SE England and current sediment toxicity was assessed using a number of techniques. Comparison of metal data to US sediment quality guidelines indicated intermediate levels of toxicity while, calculation of acid volatile sulphide to simultaneously extracted metal ratios underestimated the potential toxicity to sediment dwelling organisms. In contrast, porewater ammonia concentrations were in excess of all published ecotoxicological guidelines and indicate serious risk to biota. Re-suspension experiments were used to mimic the effects of WID on overlying water quality and ecotoxicity tests were carried out on elutriates using Daphnia magna to examine the impacts on biota. Concentrations of a range of metals in the elutriates predict that adverse biological effects would be observed during WID, however only 10% of the elutriate samples caused an adverse effect on Daphnia. Limehouse Basin is a complex aquatic environment receiving predominantly fresh waters while the sediments have high porewater chloride concentrations reminiscent of previous tidal inputs to the basin, making the choice of test organism problematic.