This paper presents the construction of a numerical three-dimensional model of the area of the Żelazny Most Mining Waste Storage Facility (MWSF). In the study area, the difficult geological conditions associated with glaciotectonics are accompanied by a complex hydrotechnical system of sediment deposition and sedimentary water drainage. In order to effectively reflect the water flow paths, a detailed schematization was carried out, using 700,000 boreholes and more than 300 hydrogeological cross-sections. In addition, numerous drainage sections, streams, and ditches were included to reliably assess the amount of saline water entering the underlying aquifers. This research was supported by magnetic resonance sounding (MRS) studies of the reservoir’s sediments. The MWSF is currently being expanded, so the work primarily focuses on illustrating changes in the hydrodynamic field resulting from the inclusion of the new southern section. Models of similar facilities have been implemented before, but in the current one, the combination of meticulous analysis of the hydro-structural system, the water balance, a significant amount of data, the size of the facility, and the use of an unstructured discretization grid in the calculations is undoubtedly innovative and will be an important contribution to the development of analogous solutions around the world.