Recent work on heavy metal pollution in Manila Bay suggests elevated concentration in the surface sediments. It is critical to identify the sources of these heavy metals to effectively rehabilitate the bay. Our study investigated the sources of the heavy metal pollution that ended up in Manila Bay and the risks associated with these toxic metals based on a recent survey conducted. Surface sediment samples with higher heavy metal concentrations were found in the upper to middle parts of the bay while lower concentrations were in the southeast areas. Multivariate analyses such as hierarchical cluster analysis (HCA), principal component analysis (PCA), and Pearson correlation analysis were used to identify the sources of the heavy metals. The heavy metal pollution in Manila Bay is attributed to several rivers draining northeast of Manila Bay, particularly the Marilao-Meycauayan-Obando River System (MMORS) which is cited as one of the 30 dirtiest river systems in the world. The ecological risks associated with heavy metals in the sediments found higher incidences of toxicity in north and middle parts of Manila Bay. Cu and Cr posed the highest risks of toxicities than any other heavy metals. Based on our analysis, the counterclockwise water gyre of the bay can explain the distribution and ecological risks associated with the heavy metals as supported by the findings of the PCA. Given the high priority by the Philippine government to rehabilitate the bay, our study strongly shows that efforts to restore the ecological status of Manila Bay will only succeed if the pollution from major rivers draining to it will be properly addressed.