AbstractNutrient breakpoints are the concentration at which there is a fundamental change in phytoplankton responses to further increases in nutrient loading. The ecological implication is that nutrient breakpoints signal a community transition from a relatively stable state to an alternate or transition state with marked changes in structure and, by extension, function. Nutrient breakpoints for the total phytoplankton community and individual phytoplankton groups in response to increases in dissolved inorganic nitrogen (DIN) concentrations were determined for two contrasting estuarine systems. Phytoplankton were exposed to increasing N addition scenarios (0–100 μmol DIN L−1) under high and low irradiance conditions. Responses of total algal biomass, group diversity, and individual algal groups were determined after 72‐h incubations in experimental bioassays. Phytoplankton from the low‐salinity estuary exhibited higher DIN breakpoints (>double) than the high‐salinity estuary while irradiance (20% vs. 40% of ambient) did not affect breakpoints. DIN additions changed algal group diversity, but community similarities were > 80%. Our results suggest that ambient DIN concentrations should not exceed breakpoint concentrations to prevent possible shifts from a stable to a transitional or alternate state. DIN thresholds should be 25 and 50 μmol L−1 for the high‐ and low‐salinity estuaries, respectively. These levels should mitigate the risk of major alterations in phytoplankton community structure and function in these two estuarine systems.