This paper is the result of hydrogeological survey engineering. Objective The development of coal resources in the Yellow River Basin has led to serious groundwater pollution. This paper summarizes the situation from the overall perspective of the basin, providing prevention and control suggestions for its sustainable and healthy development and reasonable protection of groundwater resources. Methods Starting from the strategic position of the Yellow River basin, the causes and patterns of pollution are summarized. The improved comprehensive water quality index method was used to evaluate the groundwater quality of nine major coal bases in the basin. The weighted indicators were selected using principal component analysis, and the improved Nemero pollution index method was introduced. The evaluation was conducted according to the WPI classification method. Results The research shows that through the water quality evaluation of various key sections of the Yellow River basin, it is found that the water quality results of coal bases in the basin currently account for more Class III and Class IV, with poor water quality. Currently, the pollution of highly mineralized mine water, acidic mine water, and mine water containing special components in the drainage basin is relatively large. The causes of pollution are analyzed, and the shallow and deep pollution modes of polluted groundwater are described. Conclusions We adopt corresponding prevention and control methods for three types of mine water, and propose two prevention and control technologies, paste filling technology and microbial remediation technology. Through the application of actual mines as examples, it is confirmed that pollution prevention and control technology can improve the serious problem of groundwater pollution in river basins caused by coal mining, with the hope that the research results can have reference significance for successfully promoting the rapid development of green mines in China.