The Philippines, like many other Asian countries, is struggling to combat the current widespread aquatic pollution levels caused by anthropogenic activities. Environmental biomonitoring is an efficient tool to detect and monitor the fluctuating toxicity levels in a dynamic ecosystem using bioindicators like algae, macrophytes, zooplankton, insect, bivalve mollusks, gastropod, fish, amphibians, and others to assess the extent and levels of pollution in aquatic ecosystems. The present review deliberates on the biomonitoring techniques such as bioaccumulation, biochemical alterations, population, and community-level approaches to evaluate the current status with respect to the extent and levels of pollution in the aquatic ecosystems in the Philippines which also is one of the biodiversity hotspots. Therefore, the potential applications for biomonitoring are proposed to mainly include evaluation of actual aquatic pollutions, bioremediation, toxicology prediction, and research on toxicological mechanisms. The purpose of such evaluations is to critically analyze and help stakeholders to come up with a strategic action plan with recommendations on a low-cost, sensitive, and effective bioindicator for rapid and efficient environmental biomonitoring.