The geological structure plays a crucial role in forming the chemical composition of groundwater. However, due to the diverse types, properties, and modes of combination, understanding the spatial evolution of aquifer water chemistry in relation to geological formations remains a challenging task. In this research paper, we aim to address this issue by examining the groundwater water- rock interaction and its controlling factors in two distinct aquifers: the Permian coal measure sandstone fissure aquifer (referred to as the ‘the coal measure aquifer’) and the Carboniferous limestone karst fissure aquifer (referred to as ‘the Taihui aquifer’). We employ principal component analysis and ion ratio analysis to analyze these aquifers. Furthermore, we perform a quantitative evaluation of the geological structure in the Yuanyi coal mine to explore its impact on the hydrochemical characteristics of underground aquifers. Our findings show that the main water- rock interaction in the coal measure aquifer involves cation- exchange adsorption and desulfation, while in the Taihui aquifer, it primarily entails carbonate dissolution and pyrite oxidation. We also observe variations in the complexity of faults across different parts of the study area, with the eastern part having a complexity coefficient of 0. 56, the central part 0. 61, and the western part 0. 71. With an increase in the average value of the fault complexity coefficient, the faults become more developed. As a result, the main water- rock interaction in the coal measure aquifer of the Yuanyi coal mine consists of cation- exchange adsorption and desulfation, which shows a trend towards transformation into non- carbonate leaching dissolution. Additionally, there is a further strengthening trend in the dissolution of carbonate and pyrite oxidation in the major water- rock interaction of the Taihui aquifer in the Yuanyi coal mine. These findings offer new insights and a solid theoretical foundation for studying the tectonic control mechanism underlying the chemical evolution of groundwater in concealed coalfields of North China.