Like estuaries, rivers are areas in which anthropogenic effects have its most direct influence due to increased pollution loads which triggers an increase hazard of adverse impacts. Due to the rapid changes happening in the Province of Cavite because of urbanization and unplanned land use, the river systems of Cavite becomes a dumping ground of pollutants coming from domestic, industrial and commercial sources. One of these pollutants that pose a great health hazard is the heavy metals. This paper determined the presence of heavy metal pollution in Cavite’s upland waters and its tributaries through genotoxicity assessment. The water sampling results have shown that heavy metals such as Cd, Cu, Pb, Hg and Cr are less than the method of detection limit (mdl) or above the criteria set by national government standards. This may suggest that surface waters in upland Cavite watershed are still free from heavy metal pollution. However, the detection of nuclear alterations and cellular death through necrosis and apoptosis even in low frequency in Perna viridis, a known bioindicator, demonstrated the presence of genotoxic agents possible coming from lowland watershed areas and likely manifested a highly polluted environment. It is recommended that investigation of point and non-point sources of heavy metal pollution be determined in the province’s midland and lowland watersheds.