Diverse measurements of nutrient status indicators were used to test the severity of physiological phosphorus (P) limitation of phytoplankton among lake systems ranging from oligotrophic to eutrophic, based on P and chlorophyll a (Chl a) concentrations. Metabolic assays and particulate nutrient ratios were used to estimate nutrient status at sites located in Lake Erie, Lake Ontario and Lake Huron. Variable fluorescence ratios (F v/F m), relative electron transport rates and their response to irradiance were measured by the pulse-amplitude-modulated fluorometer. Under summer stratified conditions, P deficiency was strongest in the oligotrophic sites and nitrogen (N) status indicators and Chl a variable parameters revealed no severe N deficiency. Nutrient amendment assays showed positive associations with P additions and Chl a fluorescence parameters at P-deficient sites. In the most oligotrophic sites, N additions revealed a modest increase only detected by the Chl a fluorescence parameters. Phytoplankton communities were also associated with nutrient status, where chrysophytes and cryptophytes were important in P-deficient sites and cyanobacteria, phyrrophyta, and diatoms were prevalent in nutrient-rich sites. The results confirmed that Chl a fluorescence parameters can reveal P deficiency and indicate its severity among the range of trophic status in aquatic systems.