Elimination of pharmaceuticals in source-separated human urine is a promising approach to minimize the pharmaceuticals in the environment. Although the degradation kinetics of pharmaceuticals by UV/H2O2 and UV/peroxydisulfate (PDS) processes has been investigated in synthetic fresh and hydrolyzed urine, comprehensive evaluation of the advanced oxidation processes (AOPs), such as product identification and toxicity testing, has not yet been performed. This study identified the transformation products of two commonly used antibiotics, trimethoprim (TMP) and sulfamethoxazole (SMX), by UV/H2O2 and UV/PDS in synthetic urine matrices. The effects of reactive species, including •OH, SO4(•-), CO3(•-), and reactive nitrogen species, on product generation were investigated. Multiple isomeric transformation products of TMP and SMX were observed, especially in the reaction with hydroxyl radical. SO4(•-) and CO3(•-) reacted with pharmaceuticals by electron transfer, thus producing similar major products. The main reactive species deduced on the basis of product generation are in good agreement with kinetic simulation of the advanced oxidation processes. A strain identified as a polyphosphate-accumulating organism was used to investigate the antimicrobial activity of the pharmaceuticals and their products. No antimicrobial property was detected for the transformation products of either TMP or SMX. Acute toxicity employing luminescent bacterium Vibrio qinghaiensis indicated 20-40% higher inhibitory effect of TMP and SMX after treatment. Ecotoxicity was estimated by quantitative structure-activity relationship analysis using ECOSAR.