Heavy metal pollution of a mining-impacted river—the Wenyu River—and a short section of the river it joins, the Luo River, were investigated after heavy rainfall following a dry season in March 2015 and during a normal flow season in May 2015. Water samples were collected during these two periods, and sediment samples were obtained in May as the rain washed out the sediments in March. The results showed the following: (1) The Wenyu River was severely polluted by acid mine drainage from an open-pit molybdenum (Mo) mine, and the major pollutants in the water according to Chinese national standard values were acid (pH), sulfate, Cu, Zn, Mn, Ni, and Cd. The major pollutants in the sediment were Cu, Zn, and Cd, as indicated by the geoaccumulation index and potential ecological risk index. (2) The major pollutants in the water were naturally attenuated along the river and met the national standard values after joining the Luo River, except Mn in both water samples and Cd in the samples after rain in March. The major pollutants in the sediments showed an increasing tendency along the Wenyu River and Luo River. (3) The heavy rainfall following the prolonged dry season increased acid and heavy metal contamination in the river, which might be attributed to the dissolution of efflorescent salts and the weathering and erosion of mining residues. Thus, the first heavy rain following a dry season should receive particular attention from mining enterprises and regulators. Several mitigation options and recommendations are also discussed.