We discuss the use of deterministic versus stochastic models (extinction risk concepts) providing population endpoints for decision-making in ecotoxicology. We developed a model depicting the dynamics of a trout metapopulation living in a theoretical river network, as chronic pollution occurs in one stretch of river. 1/ Deterministic endpoints seem to seriously underestimate the endangering effect of pollution on population level. The analysis of stochastic features such as extinction risk appears to be of broad interest to avoid this pitfall. 2/ Beside demographic stochasticity, random variations in the dispersal pattern adversely alter population dynamics with the increased extinction risk related to pollution perturbations. Increasing efforts are thus necessary to develop knowledge relative to stressor-induced spatial behaviours and to integrate such effects in the definition of environmental quality criteria.