Following the high rate at which many drinking water sources are polluted globally, an adequate evaluation of the potential hazards posed by polluted water systems is essential. In Nnewi urban (southeastern Nigeria), inhabitants indiscriminately dispose municipal solid wastes into streams and rivers, thereby exposing the surface water quality to deterioration. The aim of this study was to assess the pollution status, ecological risks, and probabilistic health risks of surface waters in this area using integrated study approach. Several heavy metal pollution indices used in this study showed that the waters generally have low pollution. However, Pb was identified as the priority pollutant. Ecological risk assessment revealed that the samples pose low ecological risk. Furthermore, non-carcinogenic risk assessment revealed low chronic risk; but children are more exposed to chronic risk due to ingestion than adults. However, with respect to dermal contact, all the samples pose negligible risks to both populations, as their hazard indices were <0.1. The probability of cancer risk, when compared to the acceptable range of ≤1 × 10−6 to 1 × 10−4, revealed that many of the samples pose carcinogenic risk due to Pb ingestion to adults (75%) and children (100%). However, all the samples pose negligible cancer risk due to dermal contact. Water quality index revealed that majority (75%) of the samples are poor quality water, and thus not recommended for drinking purpose. Correlation and factor analyses showed that both geogenic and anthropogenic factors influence the presence of the analytes in the surface waters.