Abstract: The continuous decrease of the water level of the “bottom aquifer” in Cenozoic is the main cause of land subsidence or shaft deformation in the eastern mining areas of China. It is an important prerequisite to manage such disasters by identifying geological conditions and influencing factors. Taking Guotun Coal Mine as the object, on the basis of analyzing the “bottom aquifer” hydrogeological conditions, the water pressure test and the Slug test are used to carry out the test analysis of its permeability, and the factors affecting its water loss are analyzed. The results show that within the scope of the industrial square, there is a large difference in the spatial distribution of the “bottom aquifer” sediments, uneven thickness, the permeability and permeability coefficients in different areas also vary greatly, and the water loss of the “bottom aquifer” in different locations is different. The main factors that lead to “bottom aquifer” loss are thawing of wellbore in early stage, roadway driving and mining disturbance of working face near wellbore in late stage.