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Nitrates are families of chemical compound that composes of nitrogen and oxygen and are one of the main sources in which plant obtains nitrogen wherein Phosphates are occurs in bodies of water containing an atom of phosphorus and oxygen. Phosphorus is essential to the development od biological organisms both in their photosynthetic and metabolic processes. On the other hand, Freshwater macroinvertebrates are any species or animals small enough to be categorized in macro that doesn’t posses a backbone. These organisms are often called exothermic or cold-blooded species. Benthic macroinvertebrates are small aquatic organisms whose habitats are under the rocks. Benthic macroinvertebrates are used to indicate water quality. In this study, we experimented whether the presence of Nitrates and Phosphates has a direct affect on these fresh water macroinvertebrates in three (3) selected sites in Wawa Dam. It turns out that not only nitrates and Phosphates can affect the biodiversity of macroinvertebrates but also the habitat they are one. The type of habitat greatly contributed to the different variety of species of macroinvertebrates in each site. In doing so, we also used the macroinvertebrates to test the water quality by using the Biotic Index Value wherein we measure the biotic value of each species.