Sustainable potable groundwater supply is crucial for human development and the preservation of natural habitats. The largest endorheic inland lake in Kazakhstan, Balkhash Lake, is the main water resource for the arid southeastern part of the country. Several ore enrichment plants that are located along its shore have heavy metal pollution potential. The study area is located around a plant that has an evident anthropogenic impact on the Balkhash Lake aquatic ecological system, with ten known heavy metal toxic hotspots endangering fragile habitats, including some indigenous human communities. This study assessed the risk of heavy metal contamination from tailing dump operations, storage ponds, and related facilities and suggested management practices for preventing this risk. The coastal zone risk assessment analysis used an innovative integrated groundwater numerical flow and transport model that predicted the spread of groundwater contamination from tailing dump operations under several mitigation strategies. Heavy metal pollution prevention models included a no-action scenario, a filtration barrier construction scenario, and two scenarios involving the drilling of drainage wells between the pollution sources and the lake. The scenario assessment indicates that drilling ten drainage wells down to the bedrock between the existing drainage channel and the lake is the optimal engineering solution for confining pollution. Under these conditions, pollution from tailings will not reach Lake Balkhash during the forecast period. The methods and tools used in this study to enable mining activity without environmental implications for the region can be applied to sites with similar anthropogenic influences worldwide.