Abstract Extreme hydrodynamic events such as flood events or dredging activities bear the risk of eroding sediments in rivers, reservoirs, harbour basins or estuaries. One of the key concerns associated with these erosion processes is the re-mobilisation of sediment-bound pollutants in highly contaminated sediments. To date, much research has been conducted to characterise flow and sediment processes associated with hydrological events such as floods. Furthermore, there is a large body of literature describing the interaction of contaminants associated with particulate matter to aquatic biota. However, there is little knowledge regarding interactions between hydro-sedimentological and ecotoxicological processes. Understanding of the ecotoxicological consequences and associated risks to aquatic wildlife associated with hydraulic events can provide critical information to regulatory bodies or managing authorities. Specifically, it will aid in assessing risks associated with current management practices and will aid in developing more sustainable future management practices for waterways or harbours. Therefore, a combined experimental methodology between hydraulic engineers and ecotoxicologists was developed to investigate the ecological and toxicological relevance of sediment re-suspension and transport during erosion. An overview of this methodology is given in the present paper.