The distribution and characteristics of seven heavy metals in sediments located in the typical ecological units (eco-units) (e.g., rivers, lakes, and estuaries) of Haihe River Basin were analyzed. The Hakanson potential ecological risk index was used for ecological risk assessment. The results indicated that the concentration scales of As, Hg, Cr, Cd, Pb, Cu, and Zn in the eco-units were 2.08 to 24.80 mg·g , 0.01 to 1135.50 mg·g , 28.70 to 152.73 mg·g , 0.03 to 195765.83 mg·g , 8.65 to 157.82 mg·g , 6.47 to 178.61 mg·g , and 21.09 to 1076.25 mg·g , respectively. The maximum concentrations of Hg, Cd, and Zn showed higher levels than other water bodies around the world. Hg and Cd have high concentrations in Zhangweinanhe River (1135.50 and 195765.83 mg·g , respectively) and Haihe Estuary (790.50 and 548.47 mg·g , respectively). According to the ecological factor, Cd and Hg showed very strong ecological risks. The seven heavy metals, namely, Cd, Hg, As, Cr, Pb, Cu, and Zn, exhibited ecological risk levels in descending order. Based on the potential ecological risk index, Luanhe River and Baiyangdian Lake had moderate ecological risks, whereas every site in Zhangweinanhe River and Haihe Estuary had substantial risk levels. The risk order of the typical eco-units are as follows: Zhangweinan River (2278345.68)>Estuary (161914.74)>Luanhe River (191.54)>Baiyangdian Lake (120.95). These results provided a scientific basis for water environment improvement and risk management of the Haihe River Basin.