In this study, groundwater, stream water, and stream sediment samples were collected from a coal mine area in Dazhu, Southwestern China, and hydrogeochemical, multivariate, and X-ray analyses were conducted to examine the effects of coal mine pollution. The groundwater and stream samples were slightly acidic to alkaline (6.7 to 8.2). Typically, the water samples were dominated by Ca2+ + Mg2+–HCO3− and Ca2+ + Mg2+–Cl−. SO42− originates from gypsum dissolution and pyrite oxidation, and Ca2+ and Mg2+ may be related to the dissolution of carbonate. According to the Chinese standard and World Health Organization guidelines, the water in the coal mine area is of good quality in terms of its physical and chemical properties, except for the concentration of Mn and Fe, with values of 1925.14 μg/L and 12,872.88 μg/L, respectively. A principal component analysis revealed two groups in which the concentration of metals and metalloids in stream sediments are affected by the coal mine drainage. The Mn and Fe average concentration in the downstream Kongjiagou drain sediment samples was 2035.1 ppm and 6%, respectively. These values were higher than the average Mn and Fe concentration in Xiaojiagou at 453.1 ppm and 2.9%, respectively. Both the Mn and Fe concentration were higher than the background values (640 ppm and 4.4%).