Phytoplankton exhibit diverse nutrient acquisition strategies, but how these influence community structure under changing nutrient regimes remains unclear – especially in nutrient-poor systems. We hypothesized that even small shifts in nutrient levels could lead to significant community restructuring. To test this, we conducted an in-situ microcosm experiment in the oligotrophic Danjiangkou Reservoir, a major drinking water source for over 110 million people. We applied gradients of nitrogen (0, 0.2 mg L⁻¹) and phosphorus (0, 0.05, 0.1, 0.2 mg L⁻¹) and monitored phytoplankton responses via biomass and diversity indices at genus and species levels. Results revealed strong phosphorus limitation: N-only additions and low P (0.05 mg L⁻¹) had minimal effects. When P exceeded 0.1 mg L⁻¹, nitrogen became the main driver of growth, with peak biomass at the highest N-P combination. Cyanobacteria and chlorophytes responded most strongly, while diatoms showed moderate increases. Margalef richness increased significantly at low P enrichment but plateaued beyond 0.05 mg L⁻¹. Shannon diversity rose with P, stabilizing at 0.1 mg L⁻¹, whereas Pielou evenness declined under high N and P, indicating dominance by a few opportunistic taxa. Microcystis proliferated under high N, while N-fixing taxa (Dolichospermum, Aphanizomenon) and Pseudanabaena dominated under N limitation. High N and rising P further promoted Microcystis and Limnothrix, while suppressing Planktothrix and Raphidiopsis. Our findings show that even modest N/P imbalances can disproportionately benefit certain taxa through species-specific traits, reshaping community structure. Effective reservoir management should consider not only absolute nutrient loads but also threshold-based responses of bloom-forming species to nutrient fluctuations.