<p>This study presents a methodology based on analytical methods for modeling the coupled mine water flow and toxic substance transport in a system of hydraulically connected workings of various sizes, depending on the drainage rate. Flow properties and velocities are calculated using hydraulic flow equations for flooded workings regarded as pipelines with distributed groundwater inflow. The non-steady mass transport from localized sources in smaller-sized workings to the withdrawal point is calculated by analytical solutions of a 1D advection–dispersion equation. The model was tested for the input data generated from the analysis of real mining sites in Ukraine, considering in detail the case of two levels of mining and the example of polychlorinated biphenyls extensively used in mining around the globe in the past. We examined the influence of the water withdrawal rate, size of workings, dilution with additional inflow along the migration path, and the source position in two levels of mining. Unlike 2D and 3D numerical transport models based on continuum mechanics, the proposed approach provides for a more realistic reproduction of mined-out space geometry and flow velocity fields. This methodology can be applied to simulate water quality evolution influenced by the contaminated water flowing from the groups of workings. It could also be helpful to calibrate large-scale numerical hydrogeochemical models of post-mining areas.</p>