This constitutes the first study to report on the reduction in toxicity of the dinoflagellate algal toxin okadaic acid after novel pulsed light (PL) treatments where ecotoxicological assessment was performed using a miniaturised format of the conventional in vivo freshwater crustacean Daphnia sp. acute toxicity test. Bivalves accumulate this toxin, which can then enter the human food chain causing deleterious health effects such as diarrhetic shellfish poisoning. This miniaturised toxicological bioassay used substantially less sample volume and chemical reagents. Findings revealed a 24-h EC50 of 25.87 μg/L for PL-treated okadaic acid at a UV dose of 12.98 μJ/cm2 compared to a 24-h EC50 of 1.68 μg/L for the untreated okadaic acid control, suggesting a 15-fold reduction in toxicity to Daphnia pulex. The bioassay was validated in this study and correlated well with the “classic” ISO format (r = 0.98) using the traditional reference chemical potassium dichromate (K2Cr2O7). Reduction by up to 65% in PL-treated okadaic acid concentration was confirmed by LC-MS/MS analysis. Findings from this study have positive ecological, societal and enterprise implications, such as the development of PL technology for the prevention or reduce algal contamination of fisheries and aquaculture industries.