Pesticides, nutrients, and ecological stressors such as competition or predation co-occur in freshwater ecosystems impacted by agricultural pollution. The extent to which combinations of these stressors affect aquatic populations and the role of nutrients availability in modulating these responses requires further understanding. In this study, we assessed how pesticides affecting different taxonomic groups and predation influence the response of Daphnia pulex populations under different trophic conditions. An outdoor experiment was designed following a factorial design, with the insecticide chlorpyrifos, the herbicide diuron, and predation by Notonecta sp. individuals as key stressors. The single impact of each of these stressors, and their binary and tertiary combinations were evaluated on D. pulex abundance and population structure under mesotrophic and eutrophic conditions for 21 days. Data were analysed using generalized linear mixed models estimated by means of a novel Bayesian shrinkage technique. Our study shows a significant influence of each of the evaluated stressors on D. pulex abundance, however, the impacts of the herbicide and predation were lower under eutrophic conditions as compared to the mesotrophic ones. We found that binary stressor interactions were generally additive in the mesotrophic scenario, except for the herbicide-predation combination, which resulted in synergistic effects. The impacts of the binary stressor combinations in the eutrophic scenario were classified as antagonistic, except for the insecticide-herbicide combination, which was additive. The tertiary interaction resulted in significant effects on several sampling dates, however, those were rather antagonistic and resembled the most important binary stressor combination in each trophic scenario. Our study shows that the impact of pesticides on freshwater populations depends on the predation pressure, and demonstrates that the combined effect of pesticides and ecological stressors is influenced by the food availability and organism fitness related to the trophic status of freshwater ecosystems.