Two pilot projects were carried out to investigate the effects of sediment remediation. One project was situated in a groyne section of the Nieuwe Merwede, a watercourse in the Rhine delta. The second was situated in a creek named Spijkerboor, which receives water from the river Meuse. For both sites it was concluded earlier that sediment pollution posed a high risk to the ecosystem. The remediations consisted of partial excavation of the contaminated sediments, followed by application of a clean layer of sandy material on top of the remaining contaminated sediment. Before and at various times after the remediation, the following investigations were carried out: physical–chemical analyses of sediment, benthic community structure observations, bioaccumulation measurements and sediment bioassays. After the remediation, a new silty sediment top layer was formed with lower contaminant levels exhibiting a lower toxicity. In the remediated site in the Nieuwe Merwede, chironomids, oligochaetes and nematodes reappeared within 3–7 months at normal densities, while in the Spijkerboor recolonization by chironomids and nematodes proceeded more slowly. After 2 years, in both the remediated sites chironomids and nematodes were present in densities much higher than before the remediation. Bivalves showed a low recolonization rate in both sites. In non-remediated, polluted reference sites also a lower sediment toxicity and a nearly comparable recovery of the benthic community was observed, probably the result of natural sedimentation of material with lower contaminant levels. Because of the natural improvement of sediment quality, the net effects of remediation were negligible in the Spijkboor. For the Nieuwe Merwede, after 2 years still lower contaminant levels were observed in the remediated site compared to the non-remediated site, resulting in lower bioaccumulation in oligochaetes. However, the contaminant levels in sediment and biota still do not meet all environmental quality objectives. Based on the outcame of this study it is recommended that the priority for remedial action is made dependent on the rate of natural covering with sediments from the rivers Rhine and Meuse.