Tropical monomictic lakes, characterized by a single annual mixing event and prolonged stratification, are particularly sensitive to climatic and anthropogenic pressures. Lake Yambo, a tropical monomictic lake in the Philippines, exemplifies such systems, with stratification prevailing during the southwest monsoon and full lake mixing occurring during the northeast monsoon. This study examined vertical and seasonal variations in environmental conditions and phytoplankton functional group composition in Lake Yambo to assess how seasonal stratification and mixing affect functional groups' vertical structure. Monthly sampling from March 2024 to February 2025 was conducted from the subsurface to 30 meters at 5-meter intervals. In situ measurements of water temperature, dissolved oxygen, pH, and nitrate (NO3-) were obtained using multiparameter probes, while chlorophyll-a, ammonia, and total phosphorus were analyzed in the laboratory. Phytoplankton samples were collected, identified, and counted, with species comprising at least 5% of the total phytoplankton biomass per period classified into their respective functional groups. Lake Yambo exhibited meso-eutrophic conditions characterized by high total phosphorus concentrations but comparatively low chlorophyll-a levels, suggesting that phytoplankton growth is likely limited by nitrogen availability. Seasonal patterns governed thermal stratification and mixing, which, in turn, regulated vertical nutrient gradients. Stratified conditions during the southwest monsoon led to nutrient trapping and hypolimnetic anoxia, while northeast monsoon mixing redistributed nutrients, particularly NO3-. These transitions strongly influenced the functional group composition. Seven dominant functional groups (B, F, G, H1, J, LO, and P) comprised 81% to 97% of the total phytoplankton biomass. Most functional groups declined with depth, but seasonal and vertical variations were distinct: Group G and H1 thrived in warmer surface waters with low nitrate concentrations. Groups J and LOwere associated with cooler, nitrate-enriched surface layers during peak mixing, while Groups B, F, and P were more abundant at deeper layers under the same conditions. These findings support the hypothesis that seasonally driven stratification and mixing in tropical monomictic lakes structure vertical nutrient availability and shape phytoplankton functional group dynamics. Notably, the bloom of Group H1 during post-peak mixing under extreme nitrogen limitation and elevated temperatures poses a health risk, as this group's descriptor taxon, Dolichospermum, can produce cyanotoxins. Thus, tropical monomictic lakes experiencing greater eutrophication may face increased risks of these toxic blooms. As a representative tropical monomictic system, Lake Yambo offers valuable insights into how similar systems respond to seasonal mixing and nutrient limitations, providing a framework for understanding and managing ecological risks in these environments.