<p>Springs are essential for water resources; therefore, it was imperative to investigate the occurrence of inorganic and emerging organic contaminants in water and sediment samples collected from three spring areas located in the Dourados River Basin (DRB), Mato Grosso do Sul (MS) State, under direct influence of soybean monoculture. Water and sediment samples were collected monthly from October (2021) to March (2022), throughout the soybean production period. The quantification of inorganic elements (Al, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Pb, and Zn) was conducted using inductively coupled plasma optical emission spectrometry (ICP-OES), while the quantification of organic emerging contaminants (ECs) was performed using liquid chromatography coupled to mass spectrometry (LC–MS/MS).The occurrence data were then used to assess the risks posed to aquatic biota by these contaminants, both individually and as mixtures present in water and sediment. Al, Fe, and Pb were found in water samples above their Brazilian environmental quality standards (EQSs), and As, Cd, Cr, Cu, and Zn also presented concentrations above their EQSs in sediments, which would represent risks to the preservation of aquatic biota. In addition, the concentrations of pesticides and bisphenol A would present risks to aquatic biota. October, November, February, and March were particularly noteworthy in terms of the prevalence of these contaminants, which coincided with the initial and final phases of the soybean cultivation cycle. Our findings offer crucial insights into spring water quality and can support the development of strategies for the conservation, mitigation, and sustainable management of water resources, including the adoption of good agricultural practices.</p>