River water heavy metal pollution has always been a hot spot problem in the field of environmental pollution prevention and control. The heavy metal content in the water of the Chenjiagou river in a stone coal mining area in Qinling exceeded the standard seriously, but the source of heavy metals was unknown, which caused trouble for pollution control. In order to find out the source and temporal and spatial changes of heavy metals in the Chenjiagou river, surface water samples such as Phase II river water, waste stone coal mine drainage and waste residue pile leaching water were collected, and the pollution index method, principal component analysis and Pearson correlation analysis methods were used to study the degree and spatial distribution of heavy metal pollution in river water, and the sources of heavy metals in river water were analyzed. The results show that the heavy metal content of the river water at the source of Chenjiagou (control point) can reach the Class I standard of surface water, and the heavy metal content in the middle reaches is significantly increased by the drainage of waste stone coal mines and the leaching water of waste residue pile in the middle reach, and the heavy metal content in the river water before entering the main stream is 3.5～312 times that of the control point; the heavy metals such as Cd, Cu, Zn, Ni, and Mn in the river water are homologous, all from the mine drainage and waste residue leaching water in the upper reaches of the river. The spatial distribution of heavy metal content in river water is related to geological bodies, pollution source distribution, river pH, salinity and other factors. The research results provide a scientific basis for the prevention and control of heavy metal pollution in Chenjiagou river.