Abstract Littoral phytoplankton and zooplankton diversity are influenced by the water quality parameters and their trophic interactions. In the largest reservoir of the Philippines, this study examined the water quality and plankton community composition in the littoral zone across three sampling sites and four depths. Of the three sites, one is located near active fish cages, one near the mouth of a tributary and one near an outlet of an upstream dam. A total of 36 phytoplankton and 34 zooplankton taxa were identified, with most taxa belonging to Chlorophyta and Cyclopoida. The most abundant phytoplankton and zooplankton taxa were Aulacoseira and Microcyclops, respectively. The three most abundant phytoplankton (Aulacoseira, Oscillatoria, Volvox) were most positively correlated with the nutrient levels [total nitrogen (TN), total phosphorus (TP) and TN:TP ratio]. A significant interaction of sampling site and depth was recorded for the phytoplankton’s Shannon diversity index and community composition. The decreased zooplankton diversity amidst decreased phytoplankton diversity in the aquaculture site aligns with the effect of lowered resource heterogeneity on zooplankton. The increased phytoplankton diversity and decreased zooplankton density and taxon richness at shallower depths were probably linked with the light availability.