The impact of pesticides on macrobenthos communities was studied on two aquatic environments in Northern Italy; River Meolo, a site exposed to agricultural pollution, and River Upper Livenza a low pollution reference site. Colonisation of artificial substrates was compared throughout the productive season. The relevance of multiple environmental stressors other than pesticides (e.g. oxygen depletion) was also assessed. Biochemical indicators (enzyme and metabolite biomarkers) were measured on selected organisms. Biomarker results (acetylcholinesterase, glutathione S-transferase, and napthylacetate esterase), as well as community structure patterns, revealed a significant difference between the two rivers. Cause-effect relationships between results and multiple stress factors were discussed.