•Long-term Chironomidae response to chemical stressors have been hardly addressed.•Model predicts Chironomidae response across generations, stages, and latitudes.•Emergence reduction stronger with prevalence of early-instar larvae.•Emergence reduction twice as severe in the 2nd year of Bti application.•Model adaptable to other insects, chemicals, latitudes via adjusted parameterisation. Chironomidae are the most abundant aquatic insect group and are important in providing energy and nutrients to aquatic and terrestrial food webs. The stress response of Chironomidae can vary with environmental conditions and time of pollutant exposure, making it difficult to understand the underlying mechanisms. Here, we use a dynamic population model to predict the potential effects of anthropogenic stressors on Chironomus riparius larvae and adult emergence for up to two years. We employed the non-chemical larvicide Bacillus thuringiensis var. israelensis (Bti) as a case study, as this stressor has been shown to reduce larval survival of C. riparius. To predict the responses of C. riparius adapted to variable geographic conditions, we simulated scenarios in which Bti is applied at three different latitudes in Europe. For each latitude, we also simulated a varying Bti application timing corresponding to a higher or a lower density of early-instar larvae, for which a higher sensitivity to Bti is documented. While acute exposure to Bti did not alter the patterns of larval development and adult emergence, in all scenarios and latitudes considered, the predicted reduction was stronger when Bti was applied to populations with a prevalence of early-instar larvae. Moreover, in all simulated scenarios, the reduction in the second year of Bti application was approximately twice as large as in the first year, revealing cumulative effects. Our model can be used to develop new hypotheses and test them through either empirical or in silico experiments to project the long-term effects of Bti on Chironomidae populations. The model can be theoretically applied to other insect groups and toxicants, and to different latitudinal scenarios by changing input parameters.