Heterosigma akashiwois a unicellular microalga which can cause massive mortality in both wild and cultivated fish worldwide, resulting in substantial economic losses. Environmental parameters such as salinity, light, and temperature showed a significant effect on bloom initiation and the toxicity ofH. akashiwo. While in previous studies a one-factor-at-a-time (OFAT) approach was utilized, which only changes one variable at a time while keeping others constant, in the current study a more precise and effective design of experiment (DOE) approach, was used to investigate the simultaneous effect of three factors and their interactions. The study employed a central composite design (CCD) to investigate the effect of salinity, light intensity, and temperature on the toxicity, lipid, and protein production ofH. akashiwo. A yeast cell assay was developed to assess toxicity, which offers rapid and convenient cytotoxicity measurements using a lower volume of samples compared to conventional methods using the whole organism. The obtained results showed that the optimum condition for toxicity ofH. akashiwowas 25 °C, a salinity of 17.5, and a light intensity of 250 μmol photons m−2s−1. The highest amount of lipid and protein was found at 25 °C, a salinity of 30, and a light intensity of 250 μmol photons m−2s−1. Consequently, the combination of warm water mixing with lower salinity river input has the potential to enhanceH. akashiwotoxicity, which aligns with environmental reports that establish a correlation between warm summers and extensive runoff conditions that indicate the greatest concern for aquaculture facilities.