The Cerrado is a hotspot for biodiversity conservation and holds the headwater springs that are major Brazilian river basins. The development of industry, agriculture, and mining causes water quality deterioration. Mathematical models appear as a management tool to simulate water quality parameters and the dispersion of pollutants in water bodies. Thus, this study aimed to evaluate the behavior of dissolved oxygen (DO) and other parameters through the QUAL2Kw (Stream Water Quality Model) model in a river in the Brazilian Cerrado. Complementary data were obtained in four experimental measurement campaigns. The calibration results showed a good fit, especially for the DO. The most critical situation occurred in October, where DO remained below 5 mg/L for a long stretch, and the ammoniacal nitrogen (NH4) and biochemical oxygen demand (BOD) presented non-compliance concerning the legal Brazilian requirements. In all campaigns, BOD remained above 5 mg/L for at least 5 km in length, disagreeing with the legislation for exceeding the distance from the mixing zone. The uncertainty analysis for the DO confirmed the critical scenario of October, and the sensitivity analysis by the Monte Carlo Simulation showed the significance of the reaeration coefficient for DO. Thus, it is concluded that the QUAL2Kw model proved dependable for the simulation of point launches in the Bois River, supplying a good fit in the calibration act. Because BOD does not meet the legal requirements in all samplings, the water use of the downstream population may be impaired by the activities found in the basin. Activities such as sand extraction, tanneries, and other food industries increase the organic burden of waterbodies and, therefore, require greater environmental inspections.