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Cyanobacterial harmful algal blooms (CyanoHABs) are an increasingly common feature of large, eutrophic lakes. Non-N2-fixing CyanoHABs (e.g., Microcystis) appear to be proliferating relative to N2-fixing CyanoHABs in systems receiving increasing nutrient loads. This shift reflects increasing external nitrogen (N) inputs, and a[50-year legacy of excessive phosphorus (P) and N loading. Phosphorus is effectively retained in legacy-impacted systems, while N may be retained or lost to the atmosphere in gaseous forms (e.g., N2, NH3, N2O). Biological control on N inputs versus outputs, or the balance between N2 fixation versus denitrification, favors the latter, especially in lakes undergoing accelerating eutrophication, although denitrification removal efficiency is inhibited by increasing external N loads. Phytoplankton in eutrophic lakes have become more responsive to N inputs relative to P, despite sustained increases in N loading. From a nutrient management perspective, this suggests a need to change the freshwater nutrient limitation and input reduction paradigms; a shift from an exclusive focus on P limitation to a dual N and P colimitation and management strategy. The recent proliferation of toxic non-N2-fixing CyanoHABs, and ever-increasing N and P legacy stores, argues for such a strategy if we are to mitigate eutrophication and CyanoHAB expansion globally.