Eutrophication is one of the greatest threats to global freshwater ecosystems. The phytoplankton responses to nutrient inputs vary in different water bodies, so it is particularly important to determine the nutrient thresholds and synergistic interactions between nutrients in different freshwater ecosystems. Field sampling and bioassay experiments were conducted to determine the thresholds of soluble reactive phosphorus (SRP), nitrate-nitrogen (NO 3 -N), and ammonium-nitrogen (NH 4 -N) in Miyun Reservoir. A separate nutrient addition bioassay was designed to assess the synergistic interactions between these nutrients. Chlorophyll a (Chl a) concentrations were used to estimate phytoplankton biomass. The results showed the following: (1) nutrient threshold bioassay indicated that eutrophication thresholds of SRP, NO 3 -N, and NH 4 -N should be targeted at below 0.04 mg P L −1 , 0.5 mg N L −1 , and 0.3 mg N L −1 , respectively, to limit the growth of phytoplankton. (2) The stimulatory effect of BNH 4 -N plus P^on phytoplankton biomass was greater than (4) Ammonium was an important factor for the growth of phytoplankton and inputs of both NH 4 -N and NO 3 -N should be reduced to control bloom formation. Our findings imply that although P load reduction is important, appropriate reductions of all forms of N in watershed is recommended in the nutrient management strategy for Miyun Reservoir.