Recent monitoring campaigns have revealed the presence of mixtures of pesticides and their transformation products (TP) in headwater streams situated within agricultural catchments. These observations were attributed to the use of various agrochemicals in surrounding regions. The aim of this work was to compare the application of chemical and ecotoxicological tools for assessing environmental quality in relation to pesticide and TP contamination. It was achieved by deploying these methodologies in two small lentic water bodies located at the top of two agricultural catchments, each characterized by distinct agricultural practices (ALT: organic, CHA: conventional). Additionally, the results make it possible to assess the impact of contamination on fish caged in situ. Pesticides and TP were measured in water using active and passive samplers and suspended solid particles. Eighteen biomarkers (innate immune responses, oxidative stress, biotransformation, neurotoxicity, genotoxicity, and endocrine disruption) were measured in Gasterosteus aculeatus encaged in situ. More contaminants were detected in CHA, totaling 25 compared to 14 in ALT. Despite the absence of pesticide application in the ALT watershed for the past 14 years, 7 contaminants were quantified in 100 % of the water samples. Among these contaminants, 6 were TPs (notably atrazine-2-hydroxy, present at a concentration exceeding 300 ng·L−1), and 1 was a current pesticide, prosulfocarb, whose mobility should prompt more caution and new regulations to protect adjacent ecosystems and crops. Regarding the integrated biomarker response (IBRv2), caged fish was similarly impacted in ALT and CHA. Variations in biomarker responses were highlighted depending on the site, but the results did not reveal whether one site is of better quality than the other. This outcome was likely attributed to the occurrence of contaminant mixtures in both sites. The main conclusions revealed that chemical and biological tools complement each other to better assess the environmental quality of wetlands such as ponds.