Changes in land use have led to important modifications in aquatic ecosystems around the world. In Brazil, extensive pastures are being converted to sugarcane crops to avoid deforestation, while the remaining pastures are being intensified to compensate for the loss of area. In this study, the hypothesis that conventional soil management practices conducted on intensive pasture and sugarcane crops increase the availability of contaminants in freshwater was tested. Thirteen mesocosms embedded in extensive pasture (EP), intensive pasture (IP), and sugarcane crops (C) systems were monitored for 392 days. The monitoring included the measurement of in situ parameters (pH, dissolved oxygen, electrical conductivity, turbidity, and chlorophyll), nutrients (total nitrogen, nitrite, nitrate, ammonium ion, total phosphorus, total dissolved phosphorus, inorganic phosphorus, and silicate), and metals (aluminum, cadmium, copper, manganese, nickel, lead, potassium, and zinc). Soil management practices were performed in IP and C treatments at full-scale (tillage, application of fertilizers, vinasse and pesticides, and cattle pasture). The patterns observed for each treatment were obtained developing Principal Component Analysis over time. The mesocosms in the EP treatment did not experience large variations in water quality over time since no soil management was performed in this treatment. However, we found that fertilizer and vinasse application was the major precursor to the deterioration of water quality over time. After the first fertilizer application, we found eight and 16 times higher concentrations of total phosphorus, and seven and 45 times higher concentrations of total nitrogen in the IP and C treatments, respectively, in comparison to their concentration in the EP treatment. The application of vinasse in sugarcane crop increased water conductivity, potassium, and manganese concentrations in mesocosms. Dissolved oxygen and pH values decreased over time in all treatments. Overall, soil management practices resulted in greater deterioration of water quality in the sugarcane treatment than in the intensive pasture.