Freshwater species are highly impacted by human activities and the consequences on ecosystem functioning are still not well understood. In the literature, a multitrophic perspective appears to be key to advance future biodiversity and ecosystem functioning (BEF) research. This paper aims at studying indirect effects of the synthetic hormone 17α-ethinylestradiol (EE2) on a freshwater food web by creating BEF links, through the interpretation of seasonal cycles and multitrophic interactions. An ecosystem model previously developed using experimental data from a unique whole-ecosystem study on EE2 was extended with the addition of Chaoborus, an omnivorous insect. During the experimental study, a collapse of fathead minnow was measured after one year of exposure. The simulation results showed that EE2 indirect effects on other fishes (horizontal diversity) and lower trophic levels (vertical diversity) were connected to multitrophic interactions with a top-down cascade effect. The results also demonstrated that adding an omnivorous, mid-trophic level group such as Chaoborus enhances resilience. Conversely, missing such a species means that the actual resilience of an ecosystem and its functioning cannot be properly simulated. Thus, the extended ecosystem model offers a tool that can help better understand what is happening after environmental perturbations, such as with EE2.