A monitoring network was established in streams within a catchment near the Costa Rican Pacific coast (2008–2011) to estimate the impact of pesticides in surface water (84 samples) and sediments (84 samples) in areas under the influence of melon and watermelon production. A total of 66 (water) and 47 (sediment) pesticides were analyzed, and an environmental risk assessment (ERA) was performed for four taxa (algae, Daphnia magna, fish and Chironomus riparius). One fungicide and seven insecticides were detected in water and/or sediment; the fungicide azoxystrobin (water) and the insecticide cypermethrin (sediments) were the most frequently detected pesticides. The insecticides endosulfan (5.76 μg/L) and cypermethrin (301 μg/kg) presented the highest concentrations in water and sediment, respectively. The ERA revealed acute risk in half of the sampling points of the melon-influenced area and in every sampling point from the watermelon-influenced area. Safety levels were exceeded within and around the crop fields, suggesting that agrochemical contamination was distributed along the catchment, with potential influence of nearby crops. Acute risk was caused by the insecticides chlorpyrifos, cypermethrin and endosulfan to D. magna, fish and C. riparius; the latter was the organism with the overall highest/continuous risk. High chronic risk was determined in all but one sampling point, and revealed a higher number of pesticides of concern. Cypermethrin was the only pesticide to pose chronic risk for all benchmark organisms. The results provide new information on the risk that tropical crops pose to aquatic ecosystems, and highlight the importance of including the analysis of sediment concentrations and chronic exposure in ERA.