Modeling community dynamics of aquatic invertebrates is an important but challenging task, in particular in ecotoxicological risk assessment. Systematic parameter estimation and rigorous assessment of model uncertainty are often lacking in such applications. We applied the mechanistic food web model Streambugs to investigate the temporal development of the macroinvertebrate community in an ecotoxicological mesocosm experiment with pulsed contaminations with the insecticide thiacloprid. We used Bayesian inference to estimate parameters and their uncertainty. Approx. 85% of all experimental observations lie within the 90% uncertainty intervals indicating reasonably good fits of the calibrated model. However, a validation with independent data was not possible due to lacking data. Investigation of vital rates and limiting factors in the model yielded insights into recovery dynamics. Inclusion of the emergence process and sub-lethal effects turned out to be potentially relevant model extensions. Measurements of food source dynamics, individual body size (classes), and additional knowledge on sub-lethal effects would support more accurate modeling. This application of a process-based, ecotoxicological community model with uncertainty assessment by Bayesian inference increased our process understanding of toxicant effects in macroinvertebrate communities and helped identifying potential improvements in model structure and experimental design.