The efforts towards reduction of nutrient contamination of surface waters have greatly gained attention to mitigate increasing incidences of harmful cyanobacterial blooms (CyanoHABs), but little attention has been paid on the roles and importance of cyanobacterial N2-fixation and phosphorus (P) scavenging pathways during cyanoHABs. Meta-transcriptomic analyses revealed that expressions of genes involved in N2-fixation (nifDKH) and P-scavenging were significantly upregulated during the bloom compared to pre-bloom in Harsha Lake. The activities of N2-fixation occurred during early summer after a late spring phytoplankton bloom, and were associated with high phosphorus and low nitrogen. The highly active cyanobacterial N2-fixers were dominated by Nostoc and Anabaena. Following the activities of N2-fixation and production of new nitrogen, an early summer Microcystis-dominated bloom, a shift of dominance from Nostoc and Anabaena to Microcystis and an increase of microcystin and saxitoxin occurred. By contrast, P-scavenging activities dominated also by Nostoc and Anabaena were associated with low P and the Microcystis bloom. This information can be used to aid in the understanding the impact that nitrogen and phosphorus have on the early summer CyanoHAB and the functional activities of Nostoc- and Anabaena-dominated or Microcystis-dominated communities, and aid in making management decisions related to harmful algal blooms.