Hospitals are one of the key contributors of pharmaceutical contaminants of emerging concern to the sewer systems. Hospitals wastewaters contain concentrations of pharmaceutical compounds between 3 and 150, which are higher than urban wastewater streams. However, dedicated treatments of the hospital effluents before discharge to the sewer system are not compulsory. Besides, conventional wastewater treatment plants have not been designed to remove pharmaceutical compounds effectively, and consequently, these micropollutants can reach the aquatic ecosystems. The removal of pharmaceutical compounds in real hospital wastewater was gaged using three different microbial cultures (white rot-fungus Trametes versicolor, microalga Isochrysis galbana, and a mixed culture of non-sulfur purple phototrophic bacteria). Before and after bioassays of the hospital wastewater, environmental hazard quotients were used to evaluate the biological treatment efficiency. Up to 45 out of the 79 compounds included in the analytical method were noticed in the hospital wastewater, with a predominance of analgesics/anti-inflammatories (acetaminophen, ibuprofen, ketoprofen, and naproxen). It was followed by antibiotics (azithromycin, ciprofloxacin, and ofloxacin, out of which the first two are included in the watch list of substances for monitoring in water in 2020) and anti-hypertensive drugs. Isochrysis galbana reached a reduction of 45% of the total concentration of pharmaceuticals, whereas Trametes versicolor and mixed culture of purple phototrophic bacteria improved the reductions up to 69% and 76%, respectively. Moreover, potential environmental risk compounds (antibiotics, particularly ciprofloxacin and ofloxacin) were removed by Trametes versicolor in higher extension, obtaining a total hazard quotient reduction higher than the other two cultures. Removal efficiency and environmental risk assessment of remaining PhACs were used to evaluate the performance of the new biological systems for the treatment of emerging pollutants. According to both criteria, T. versicolor seems the most capable alternative for removing pharmaceutical compounds in hospital wastewater effluents.