In the present study, a pilot-scale ozonation system was introduced as post treatment to reduce the pharmaceuticals and toxicity in the effluent of a pilot-scale Moving Bed Biofilm Reactor ( MBBR) treating hospital wastewater. The ozonated effluent was polished further by suspended biofilm carriers to remove biodegradable organic matter and toxicity generated from ozonation by-products. A laboratory ozonation system was used to mimic the experiments, which were carried out at the pilot plant so that the removal of pharmaceuticals in the pilot and laboratory experiments could be compared. Delivered ozone dose achieved 90% removal of pharmaceutical was obtained and it was normalised to dissolved organic carbon (DOC). These normalised results show that trimethoprim was eliminated by ozone easier than other pharmaceuticals. Fluorescence was found to be highly correlated to the removal of pharmaceuticals, and fluorescence with a wavelength of 275 nm of excitation and 310 nm of emission had the closest correlation. After polishing MBBR was introduced into the ozonated wastewater, half of its protein-like fluorophore was removed. The toxicity of the hospital wastewater during MBBR treatment was measured by Vibrio fischeri, the inhibition of which decreased from 80% to 50%. By applying ozonation, this inhibition reduced to 20%.