Previous work suggests that a high rate of internal ferrous iron (Fe2+) loading from anoxic sediments into overlying waters favours cyanobacteria dominance (>50% of the phytoplankton biomass) over eukaryotic algae. This Cyanobacteria–Ferrous conceptual model was assessed along the Georgian Bay coastline of Lake Huron, Ontario, in one meso-eutrophic and three oligotrophic embayments that experience natural hypolimnetic anoxia. Cyanobacteria dominated all embayments in the relatively warmer summer of 2012 but not in the much cooler summer of 2014, although hypolimnetic anoxia and internal Fe2+ loading were observed in both summers in all embayments. A cyanobacteria bloom large enough to turn the lake visibly green was observed only in warmer 2012 in the meso-eutrophic embayment. Results show that warm summer temperatures and internal Fe2+ loading are necessary preconditions for cyanobacteria dominance, while high nutrient levels are needed to form large blooms. There were no consistent patterns between dominance and total and dissolved phosphorus (P), total nitrogen, ammonium, and nitrate. Internal P loading was not a necessary precondition for dominance. While P removal programs will decrease phytoplankton biomass in eutrophic waters, oxidized surficial sediments must be maintained throughout an aquatic system to prevent cyanobacteria dominance.