Evaluating the effects of chemical contamination on populations and ecological communities still constitutes a challenging necessity in environmental management. However the toxic effects of contaminants are commonly measured by means of organism-level responses. Linking such effects measures with ecological models is a promising way to apprehend population-level impacts. In this way, population models are currently increasingly used in predictive risk assessment procedures, but their use in environmental diagnostic framework remains limited due to their lack of ecological realism. The present study with the crustacean amphipod Gammarus fossarum, a sentinel species in freshwater monitoring, combines a dual field and laboratory experimental approach with a population modelling framework. In this way, we developed an ecologically-relevant periodic matrix population model for Gammarus. This model allowed us to capture the population dynamics in the field, and to understand the particular pattern of demographic sensitivities induced by Gammarus life-history phenology. The model we developed provided a robust population-level assessment of in situ-based effects measures recorded during a biomonitoring program on a French watershed impacted by past mining activities. Thus, our study illustrates the potential of population modelling when seeking to decipher the role of environmental toxic contamination in ecological perturbations.