This study assessed the distribution of five heavy metals (Cd, Pb, Cu, Zn, and Fe) across the various stages of treatment in three selected sewage treatment facilities and their receiving waterbodies in the Eastern Cape Province, South Africa. Aqueous and solid (sludge) samples were collected monthly from September 2015 to February 2016. Quantitation was achieved by atomic absorption spectrometry after necessary sample preparations. Concentrations of heavy metal cations in the sludge generally varied from <DL (below detection limit) to 1.17 mg kg−1, <DL to 0.14 mg kg−1, 27.588 to 69.789 mg kg−1, and <DL to 0.099 mg kg−1 for Cu, Cd, Fe and Pb; while Zn was below detection all through. Similarly, the levels of Cu, Cd, and Fe in the influents, effluents, upstream and downstream across the three plants ranged from <DL–6.588 mg L−1, <DL–0.636 mg L−1, <DL–0.878 mg L−1 and <DL–0.711 mg L−1, respectively; Zn and Pb were less than DL in all the matrices and study locations. All the contaminants were below hazardous levels in all the sludge and aqueous samples except Cd which was higher in effluents and surface waters across the board. Wastewater Treatment Plant (WWTP)-A exhibited better removal capacity for Fe (86.6%), compared to WWTP-B (34.7%) and WWTP-C (56.9%). However, the removal of Cu and Zn was very poor in all the treatment facilities studied. Carcinogenic and non-carcinogenic risks evaluated were sufficiently low. This suggests that the levels of contamination, even with respect to Cd, was minimal. Nevertheless, efforts should be made to keep the concentrations of these contaminants at levels safe for humans and aquatic organisms. Furthermore, the use of the effluents from these facilities for irrigation should be discouraged to prevent unnecessary build-up of metals in the soil and plants grown with such, as well as subsequent bioaccumulation and biomagnification in the food chain.