The absence of species in polluted sediments does not necessarily imply exclusion due to toxicity. Other factors, like for instance food availability and oxygen content, could also partly cause their absence. Hence, knowledge of the (combinations of) factors acting on individual organisms is essential in order to understand how populations can persist in polluted sediments. In this study species-specific responses of two benthic invertebrate species, the mayfly Ephoron virgo and the midge Chironomus riparius, to environmental variables were compared. It was assessed how these responses determine the distribution of these species in polluted sediments. Subsequently, it was discussed how these results can assist in the formulation and implementation of policies with respect to the ecological risks of pollution to benthic invertebrates. The present study showed that sediment pollution is likely to act only occasionally as a single selective force reducing the persistence of sensitive species. Yet, it was shown in our studies that the pollution level in some tested sediments limits the persistence of insects with the sensitivity of E. virgo. In other cases, however, a combination of conditions is likely to determine their persistence. As shown here for C. riparius, sediment pollution drives this species close to intoxication, but a high availability of food enables them to persist very well. The present study provides evidence that pollution levels exceeding current Dutch Negligible Concentrations may pose a detectable ecological effect at least for sensitive benthic invertebrates.