Abstract: Accurate identification of the source of water gushing in closed coal mines and correct division of water gushing modes are of great significance for scientific disposal of water resources waste and water environment pollution caused by closed coal mine drainage. A comprehensive method for water inflow characterization, source identification, and model research for closed coal mines by multivariate analysis of “water quantity–hydrochemistry–microorganism–hydrogeological conditions” is proposed. The method is based on the dynamic monitoring data of water inflow and the water chemical and microbial indexes of several closed coal mines in the Songzao mining area of Chongqing in a hydrological year. Water quality analysis methods, such as flow dynamic analysis of water inflow and flow–rainfall hydro-logical series correlation function, descriptive statistics of water chemical indexes, and the Pearson correla-tion function of water chemical indexes between mine water samples are also used as bases. The method is further coupled with the hydrogeological conditions of the mining area. Results show that there are three types of fluctuations in the response of water inflow from closed coal mines to rainfall: sudden rise and slow drop, slow rise and slow drop, and stable. The difference in water inflow source and water diversion medium is the main reason for the dynamic change in mine water inflow and the temporal and spatial differences in its response to rainfall. It also causes the characteristics of large variability in TDS, pH, chemical correlation degree, and microbial content of mine water. Based on water source identification, four types, rainfall infiltration type, aquifer release type, old empty water overflow type, and compound type, of water gushing modes of closed coal mines in mining areas are proposed. The multivariate comprehensive analysis method identifies the source of water inrush from closed coal mines in karst mining areas effectively, deepens the understanding of the characteristics of water inrush from closed coal mines, and provides theoretical support for the scientific prevention and control of closed coal mine water inrush in Songzao mining area and the coordinated development of environment and resources.