Understanding the effects of anthropogenic pollutants at the ecosystem level requires a proper understanding of the toxicological effects at the population level. Species living in estuaries resist highly fluctuating conditions, and are often exposed to sublethal concentrations of pollutants coming from industrial and domestic wastes. In the Westerschelde estuary, the most upstream sampled population of the nematode Pellioditis marina is genetically less diverse than elsewhere. It experiences lower salinities and higher Cd concentrations than more downstream populations in the estuary. In the present study, we investigate whether these environmental conditions may explain the lower genetic diversity in the most upstream location. To this end we followed the development of genetically diverse P marina populations under experimental conditions during 14 days. Genetic diversity was assessed in the F1, F2 and F5 generation by screening mitochondrial cytochrome oxidase c subunit 1 variation with the single-strand conformation polymorphism method (SSCP) and nucleotide sequencing. Our results show that sublethal Cd concentrations reduce population development of P. marina at suboptimal salinities, and that low salinity conditions induce responses at the genetic level. Nevertheless, the genetic effects were not persistent over generations, which emphasize the need for longer multigenerational experiments. (c) 2007 Elsevier B.V. All rights reserved.