Seasonal fluctuation patterns of the neurotoxic amino acid β-N-methylamino-L-alanine (BMAA) were examined at four-day intervals during the ice-free season in water at three nearshore stations in the south basin of Lake Winnipeg, Canada. BMAA patterns were significantly exponentially correlated with concurrent phaeophytin, and inversely with chlorophyll a, indicating that free BMAA concentrations increased as blooms declined. BMAA was also significantly related to preceding microcystin concentrations, and as chlorophyll a declined, the proportion of BMAA relative to microcystin increased. Cross correlations identified significant relationships between BMAA and immediately preceding nitrate-N/inorganic phosphorus ratios, nitrate-N, rainfall, and a marginal inverse correlation with inorganic phosphorus. Total suspended solids levels were also significantly associated with BMAA, likely due to shading effects. A very high BMAA concentration was found under collapse of intense bloom conditions. These results have implications for water quality monitoring, nutrient management strategies and public health.