Aquatic environmental deterioration is becoming a serious problem due to rapid urbanization and economic development, particularly in developing countries. As two important components of the aquatic environment, water quality and sediment pollution are widely considered to be concerns; however, they are considered separately in most cases. The relationship between water quality and sediment pollution with heavy metals has been little addressed. In this study, the Haihe River Basin (HRB), one of the most polluted areas in China, was used as a case study, and the eutrophication index (EI) and the potential ecological risk index (RI) were employed to evaluate water quality and sediment pollution of heavy metals, respectively. The results showed that generally in the HRB, the water quality was poor, while the risk of heavy metal pollution was relatively low. Surface water quality was mainly influenced by sewage discharges from human daily life, and heavy metal pollution was affected by industry structure, in that the areas with resource/energy consumption industries and high-pollution industries often have high risks of heavy metal pollution Synergic pollution from water eutrophication and sediment pollution with heavy metals was found, especially in the central areas of the HRB, and it was largely dependent on the type of human activities. In the places with intensive human activities, such as secondary industry, eutrophication occurred simultaneously with heavy metal pollution, other than in less human-affected areas. These findings are useful for planning aquatic environment protections and river ecosystem management.