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Over the last 22 years significant phytoplankton changes in Hongfeng lake reservoir have been observed with multiple years of harmful cyanobacteria blooms (cHABs). Fish farming and other anthropogenic activities from 1994-2001 triggered the harmful blooms. Nine years after the cessation of aquaculture, a conversion from problematic species (Microcystis spp, Aphanizomenon flos-aquae) to the less problematic species P. limnetica and other associated non-cyanobacteria taxa was recorded. Through this period of change, trophic factors (bottom-up) were re-examined, and correlations between cHABs and selected environmental variables were observed. Higher temperatures, nutrients (TN, TP) and available light significantly favored the development of Microcystis spp blooms. With declining nutrient loads, and a decline in TP relative to TN there was a competitive shift from Microcystis summer blooms to the growth of Pseudanabaena limnetica and other non-cyanobacteria. Pseudanabaena limnetica was favored over Microcystis spp when temperatures were <20°C and TP was <0.03 mg L-1. The apparent species succession to P. limnetica was enhanced by a competitive advantage under varied light conditions. Multiple environmental and biotic conditions (not always nutrients) were driving cHABs. Although only a selected number of environmental variables were examined, the CCA analysis supports observations that temperature and nutrients were associated with the species shift. The replacement of cHABs with the growth of less toxic cyanobacteria like P. limnetica, and other algae creates an interesting scenario (new community condition) for the removal of problematic taxa in reservoir systems. Diverting or controlling blooms will have direct implications on water quality and economic remediation initiatives in reservoir and lake management.