Grand Lake St. Marys (GLSM) is a large, shallow, hypereutrophic lake situated in an agricultural watershed with high-nutrient, non-point source runoff. The resulting harmful algal blooms (HABs) are typically dominated by Planktothrix, which can produce microcystin, a potent cyanobacterial toxin that has varied in concentration over the past decade. Some drivers of bloom biomass and toxicity in GLSM are described, but recent years (2019–2022) have exhibited anomalous combinations of winter ice cover and spring runoff, suggesting that additional factors contribute to variability in HAB severity and toxicity. 2020 and 2022 were typical water years, with normal tributary runoff volumes occurring primarily in late winter and spring after either little to no ice cover (2019–2020) or heavy/prolonged ice cover (2021–2022). However, 2021 exhibited prolonged winter ice and low winter/spring runoff. 2020 and 2022 were typical bloom years, with near monoculture, Planktothrix-dominated biomass (11 to 405 μg/L total chlorophyll) and high total concentrations of microcystins (<0.3 to 65 μg/L). However, the first half of 2021 exhibited lower biomass (18 to 65 μg/L chlorophyll a) and toxin concentrations (0.4 to 2.0 μg/L). While biomass returned to bloom levels when external tributary loading increased, ammonium uptake and regeneration rates and microcystin concentrations remained low throughout 2021 (in contrast to other years). Overall, potential ammonium uptake rates strongly correlated with chlorophyll and microcystin concentrations (Bayesian R2 = 0.59; 95% CI = 0.44 to 0.65). Phytoplankton diversity was higher in 2021 than other years, especially in spring/early summer, with increased dinoflagellates and diatoms in spring, followed by a mixed cyanobacterial assemblage in summer. These results suggest that lower external nutrient loads can drive immediate positive impacts on water quality, such as reduced HAB biomass and toxicity and higher phytoplankton diversity, even in hypereutrophic, shallow lakes.