The stability of water supply systems is one of the main factors for reliable operation of large industrial complexes. This problem is considered through the case of the Azot branch of JSC URALCHEM in the city of Berezniki, which derives raw process water from the Kama River (Kama storage reservoir). A characteristic feature of this water body is a highly variable hydrological regime. During the summer low water period, it is characterized by low current velocities. In winter, when the water level in the reservoir declines, a typical river flow regime is observed. In addition, the water body is exposed to heavy human impact. The bulk of the load comes from non-declared non-point (diffuse) sources. Their characteristic feature is high suspended solids content, and, accordingly, the density of the effluents. Their behavior is fundamentally different from the processes of dilution and migration of effluents with neutral buoyancy. Traditional methods of calculating dilution processes cannot be used to describe them. A two-layer flow is formed, where the content of basic ions in the surface horizon is more than an order of magnitude lower than near the bottom. Early in July 2020, a significant increase in the content of chlorine and sodium ions was observed at the water intake facility of the Azot branch, causing a shutdown of the plant. The causes of the phenomenon had to be identified. The putative causes were emergency discharges of concentrated waste from the sludge dump on the shore or contamination by the wastewater entering the Kama River below the intake facility due to backflow. These situations can be modeled taking into account the vertical heterogeneity of water masses based on the coupling of hydrodynamic models in one-, two-, and three-dimensional formulation. As a result, it was shown that the only cause of the emergency could be water intake from the Kama River bottom flow.