To address questions regarding the potential impact of elevated total phosphorus (TP) inputs (due to relaxed regulations of TP loading), a series of TP enrichment experiments were conducted at pelagic stations in the 3 hydrologically distinct basins of Lake Erie. Results of nutrient assimilation measurements and assays for nutrient bioavailability suggest that the chemical speciation, and not concentration, of nitrogenous compounds may influence phytoplankton community structure; this in turn may lead to the selective proliferation of cyanobacteria in the eastern basin of the lake. Assays with cyanobacterial bioluminescent reporter systems for P and N availability as well as N-tot:P-tot assimilation ratios from on-deck incubation experiments support this work. Considered in the context of a microbial food web relative to a grazing food web, the results imply that alterations in current TP loading controls may lead to alterations in the phytoplankton community structure in the different basins of the Lake Erie system.