Historical pesticide use in agriculture and trace metal accumulation have long term impact on soil, sediment, and water quality. This research quantifies legacy and current-use pesticides and trace metals, assessing their occurrence and toxicological implications on a watershed scale in the Sogamoso River basin, tributary of the Magdalena River in Colombia. Organochlorine pesticides (22), organophosphates (7), and azole fungicides (5), as well as trace metals cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), nickel (Ni), lead (Pb), and zinc (Zn) were analyzed in croplands and along the river. Toxic units (TU) and hazard quotients (HQ) were calculated to assess the mixture toxicity. Organochlorines were detected in 84% of soils, 100% of sediments, and 80% of water samples. Organophosphates were found in 100% of soil and sediment samples, as well as in 70% of water samples. Azole fungicides were present in 79% of soils, 60% of sediments, and in 10% of water samples. Total pesticide concentrations ranged from 214.2 to 8497.7 μg/kg in soils, 569.6–12768.2 μg/kg in sediments, and 0.2–4.1 μg/L in water. In addition, the use of partition coefficient (Kd) and organic carbon fraction (foc) allowed the distribution analysis for most of the pesticides in sediments, suspended particulate matter (SPM), and water systems, but not for soils. Concentrations of trace metals Cu, Zn, Pb, and Zn exceeded international quality guidelines for agricultural soils in 16% of the samples. Furthermore, Cu and Zn concentrations exceeded sediment quality guidelines in 50 and 90% of the samples, respectively. These findings demonstrate the broad distribution of complex mixtures of trace metals, legacy organochlorines, and current-use pesticides across the basin, indicating that conventional agriculture is a significant source of diffuse pollution. Sustainable agricultural practices are needed to mitigate adverse impacts on ecosystems and human health. © 2024 Elsevier Ltd