Lake Mainit is considered an important communal resource in the provinces of Surigao del Norte and Agusan del Norte, which makes the lake a rich natural resource with great ecological value. Calculations of contamination factor (Cf), enrichment factor (Ef), degree of contamination (Cd), modified degree of contamination (mCd), and ecological risk index (MRI) were utilized to diagnose the level of anthropogenic and environmental risk of heavy metal accumulation in bottom sediments. Cf throughout all stations indicates that Lake Mainit is highly contaminated with Ni. Ef mainly was greater than one across all stations, with extremely severe enrichment of Ni. Ni and Cr have a high degree of contamination among all stations. The general MRI across all stations of Lake Mainit is at very high risk. It is evident that Lake Mainit is polluted and will continue to be polluted if fast and reliable responses, both for monitoring and environmental protection, are not provided. Hence, there is a need for comprehensive management of Lake Mainit to help restore its health both from the residents and the acting LGUs of the surrounding municipalities of Lake Mainit.