Surface waters such as lakes and rivers are utilized by many individuals for domestic use including drinking. However, waterborne disease outbreak due to poor quality water of these natural resources has continually caused high morbidity and mortality rates in many areas of the world. Our study focuses on assessing the microbial quality of water in Lake Lanao along Marawi City, Lanao Del Sur, Mindanao, Philippines. We used Heterotrophic Plate Count (HPC) to determine the general load of heterotrophic bacteria and Multiple Tube Fermentation for total coliform count and determine the presence of the fecal coliform, E. coli. We also run a household survey covering the inhabitants’ use of the lake’s water and self-reported waterborne-related diseases to trigger formulation of right actions in relation to the resulting water quality. Our results showed positive presence of the mentioned water quality indicator bacteria that goes beyond the accepted value of HPC (HPC >500 CFU/ml) and MPN (MPN >16/100ml). These figures indicate that Lake Lanao has poor microbial quality of water and could be risky for human use and consumption. Our team recommends improvement of sources for safe drinking water and sanitation, health teaching with high emphasis on boiling the water prior to use, and further development of this research which includes regular monitoring, identification of specific type of microbial indicators, and correlational studies.