Anthropogenic interference the ecosystem unavoidably changes the physical and biological environment. The biodiversity of the Amazon region has been threatened by increased agricultural production and pesticide use. Considering that monitoring pesticides in environments close to their application is one of the ways to preserve the ecosystem, this study investigated the levels of pesticide residues in different environmental compartments (soil, sediment, and water samples). Thirty-one active ingredients of pesticides of different classes were analyzed by UHPLC-MS/MS. For this purpose, we performed quarterly collections in dry and rainy seasons in the region, which helped to evaluate the impact of pesticides on the biodiversity of the study site. Sampling points were the river banks in the area of an agricultural project in Formoso do Araguaia city, Tocantins State. After analysis, we detected the following substances in the water matrix: clomazone, fluazifop-p-butyl, flutolanil, metsulfuron-methyl, propanil, and imidacloprid. Nevertheless, we did not detect any active ingredient in sediment and soil matrices. The active ingredient clomazone was present in all points in the trials, with concentrations reaching up to 0.538 μg L-1. These substances have potential for groundwater contamination. Even at low concentrations in the aquatic ecosystem, these substances can damage human populations and wildlife species, given their toxicological classification. Thus, the study showed an environmental risk of bioaccumulation and/or biomagnification in the region, which may affect environmental biodiversity as well as human health.