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The total cultivated area in Brazil reached to 62 million ha in 2018, with the predominance of genetically modified soybean and corn (36 and 17 million ha, respectively) in no-tillage systems. In 2018, 5.3 × 105 Mg of active ingredient of pesticides was applied in cropfields, representing about 7.3 L of commercial product by habitant. However, the monitoring of water courses contamination by pesticides remains scarce and is based on traditional grab sampling systems. In this study, we used the grab (water) and passive sampling (Polar Organic Chemical Integrative Sampler—POCIS) to monitor pesticide contamination in the river network of a representative agricultural catchment of southern Brazil. We selected 18 sampling sites located in tributaries and in the main course of the Guapore River, in Rio Grande do Sul State, with different land use predominance including forest, urban, and agricultural areas. Altogether, 79 and 23 pesticides were, respectively, analyzed in water and POCIS samples. The water of Guapore River and its tributaries were highly contaminated by many pesticides, especially by four herbicides (2,4-D, atrazine, deethyl-atrazine, and simazine), three fungicides (carbendazim, tebuconazole, and epoxiconazole), and one insecticide (imidacloprid). The amount, type, and concentration of pesticides detected were completely different depending on the sampling technic used. POCIS was effective to discriminate the contamination according to the main land use of each sampling site. The monitored areas with the predominance of soybean cultivation under no-tillage tended to have higher concentrations of fungicide, while in the more diversified region, the herbicides showed higher values. The presence of five herbicides used in corn and grassland forage production was correlated with areas of integrated crop-livestock systems, in contrast to higher contamination by 2,4-D in areas of intensive production of soybean and winter cereals.