Abstract The harmful algal bloom species Prymnesium parvum has caused millions of dollars in damage to fisheries around the world. These fish kills have been attributed to P. parvum releasing a mixture of toxins in the water. The characterized toxins, reported as prymnesin-1 and -2, have structural similarities consistent with other known ionizable compounds (e.g., ammonia). We investigated whether pH affects the toxicity of P. parvum under conditions representative of inland Texas reservoirs experiencing ambient toxicity from bloom formation. We evaluated pH influences on toxicity in laboratory and field samples, and modeled the physicochemical properties of prymnesins. Aquatic toxicity to a model fish and cladoceran was reduced by lowering pH in samples obtained from reservoirs experiencing P. parvum blooms; similar observations were confirmed for experiments with laboratory cultures. A pKa value of 8.9 was predicted for the prymnesins, which suggests that ionization states of these toxins may change appreciably over surface water pH of inland waters. These findings indicate that ionization states of toxins released by P. parvum may strongly influence site-specific toxicity and subsequent impacts to fisheries. Consequently, these results emphasize the importance of understanding processes that affect pH during P. parvum blooms, which may improve predictions of ambient toxicity.