Interactive effects of stoichiometry and environmental variability regulate cyanobacteria toxicity in two eutrophic bays

Abstract Cyanobacteria blooms are a leading threat to water quality globally. Despite this, the timing and frequency of toxin production associated with harmful blooms are not well understood. Here we explore cyanobacteria bloom dynamics and cyanotoxin production in two heavily instrumented shallow, eutrophic bays of Lake Champlain through the lens of ecological stoichiometry. We use nutrient resource supply ratios (DIN : TP), seston nutrient ratios (C : N : P), and high‐frequency buoy data to explore which nutrients limit cyanobacteria growth across the bloom season, how seston nutrient ratios relate to cyanotoxin production, and which environmental conditions trigger bloom development. We identified differences in limiting nutrients across the season, where Missisquoi Bay was mainly phosphorus limited, and St. Albans Bay was nitrogen limited. Despite differences in biomass and severity of the cyanobacteria blooms, microcystin and anatoxin concentrations did not differ between each bay. Additionally, microcystin production only occurred when seston C : N ratios indicated low to moderate nitrogen limitation (C : N < 14.6), supporting experimental findings that toxin synthesis may be tightly coupled with seston C : N : P elemental ratios. Taken together, these results highlight the complex interplay between nutrient cycling and environmental conditions in selecting functional traits of cyanobacteria that determine cyanobacteria bloom evolution and cyanotoxin production. Our study provides a comprehensive exploration of cyanobacteria blooms through the lens of ecological stoichiometry coupled with high‐frequency monitoring that explains the divergence in bloom severity between two shallow, eutrophic bays of Lake Champlain.