Abstract The resilience of cyanobacterial blooms challenges lake restoration programmes based on nutrient load reduction. The survival of organisms may depend on episodic short‐term fluctuations of nitrogen (N) and phosphorus (P). Insight into physiological responses to shifts in nutrient limitation will improve our understanding of cyanobacterial bloom resilience. This study investigated the resilience and collapse of a long‐term cyanobacterial bloom dominated by Planktothrix agardhii and Raphidiopsis mediterranea, subjected to different periods of dissolved inorganic nitrogen (DIN) and phosphorus (SRP) inputs in Lago Rodó, a polymictic, hypereutrophic (6.0 ± 1.6 μmol total P/L) and turbid lake (attenuation coefficient: 4.7 ± 1.7 m−1). Phytoplankton composition, nutrient dynamics and physiological monitoring of [32P] phosphate uptake kinetics were studied over four summers. The influence of environmental nutrient supply on phytoplankton net phosphate uptake kinetics was analysed with a flow–force model that gives the threshold value of phosphate uptake ([Pe]A), a limiting concentration below which incorporation is not energetically possible by organisms, and the membrane conductivity coefficient (LP). The [Pe]A reflects the affinity and LP the activity of the cellular uptake systems. Nutrient supply into the lake sustained high DIN:SRP ratios and high cyanobacterial biomass that showed P‐deficiency features characterised by low [Pe]A (5.4 ± 0.5 nm [32P] phosphate) and high LP. High cyanobacterial biomass persisted after external nutrient inflows were interrupted for 14 months, which resulted in low dissolved DIN:SRP ratios; however, N2‐fixers did not develop. The collapse of cyanobacterial populations occurred under the lowest N:P ratios, low affinity and activity of phosphate uptake systems and strong water outflows. Our study suggests that the alleviation of N‐deficiency under high N:P ratios enhances the activation of phosphate uptake systems by cyanobacteria. The flexible physiological response results in more efficient exploitation of limiting nutrients favouring cyanobacterial resilience under suboptimal conditions.