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Phosphorus (P) availability frequently limits primary production in lakes, influences the physiology of phytoplankton, shapes community structure, and can stimulate or constrain the formation of cyanobacterial blooms. Given the importance of P, numerous methods are available to assess P stress in phytoplankton communities. Marine phytoplankton are known to substitute sulfolipids for phospholipids in response to P limitation. We asked whether sulfolipid substitution might serve as an additional indicator of P stress in freshwater phytoplankton communities. The question was addressed using cultures ofMicrocystis aeruginosa, Lake Erie microcosms, and surveys of lipid profiles in Lake Erie during aMicrocystisspp. bloom. Peak area response ratios of the intact polar lipids sulfoquinovosyldiacylglycerol (SQDG) to phosphatidylglycerol (PG) were used as the metric of lipid substitution. In cultures ofM. aeruginosaNIES‐843, the SQDG : PG ratio increased from ~ 0.9 to ~ 3.3 with decreasing P concentration. In P‐limited communities, the SQDG : PG ratio increased from ~ 6 to ~ 11 after 48 h in microcosm controls, while P amendments reduced the ratio to ~ 3. In Lake Erie surveys, the SQDG : PG ratio ranged from ~ 0.4 to ~ 7.4 and was negatively correlated (Pearsonr = −0.62) with total dissolved P. The SQDG : PG ratio was not correlated with concentrations of chlorophylla, soluble reactive P, or N : P molar ratios. These results demonstrated thatM. aeruginosaandMicrocystis‐dominated communities remodel lipid profiles in response to P scarcity, providing a potential short‐term, time‐integrated biomarker of nutrient history and P stress in fresh waters.