Significant evidence is available in the literature justifying the search for treatment technologies or process combinations to improve the decomposition of dozens of pharmaceuticals in wastewater. Conventional processing techniques are insufficient in removal of the pharmaceuticals, for having resistant waste and low biodegradability. Electron beam irradiation (EBI) may play an important role in this context, and relatively low doses have been reported for such purposes. The objective of this study was to apply the process of irradiation with electron beam in order to reduce the toxic effects of fluoxetine, propranolol, and a binary mixture of these pharmaceuticals in aqueous solution. Ecotoxicological tests conducted in two model organisms, Daphnia similis microcrustacean, and Vibrio fischeri bacterium. It was observed that D. similis was more sensitive to the pharmaceuticals and binary mixture, when compared to V. fischeri. When EBI was applied, all doses showed significant reduction of toxicity for D. similis, and the opposite for V. fischeri, when only 5.0 kGy showed a significant reduced of toxicity for the pharmaceuticals and binary mixture. 5.0 kGy was the best removal efficiency for toxicity, approximately 80% for D. similis and 20% for V. fischeri.