Contaminated sediment in the river basin has become a source of pollution with increasing importance to the aquatic ecosystem downstream. To monitor the temporal changes of the sediment bound contaminants in the River Elbe and the River Dommel monthly toxicity tests were applied to layered sediment and river water samples over the course of 10 months. There is an indication that contaminated sediments upstream adversely affected sediments downstream, but this process did not cause a continuous increase of sediment toxicity. A clear decrease of toxic effects in water and upper layer sediment was observed at the River Elbe station in spring related to high water discharge and algal blooms. The less obvious variation of sediment toxicity in the River Dommel could be explained by stable hydrological conditions. Future monitoring programmes should promote a more frequent and intensive sampling regime during these particular events for ecotoxicological evaluation.