Feasibility for removal of two commonly used antibiotics (amoxicillin and ciprofloxacin) from hospital wastewater was experimentally investigated using sub- and super-critical water oxidation. Effect of temperature and flow rate on the concentration of antibiotics was observed in the temperature range from 473K to 773K and at flow rates of 3 and 5mL/min. Samples were analyzed in terms of their total organic compound (TOC) and chemical oxygen demand (COD). Highest COD reduction was achieved at the highest temperature of 773K, where it was reduced for 76%. Furthermore, the highest decrease in TOC was 63% at 773K. Using liquid chromatography tandem-mass spectrometry (LC–MS/MS) amoxicillin and ciprofloxacin were identified and the structure of products was assigned by MS fragmentation patterns. An activated sludge respiration inhibition test demonstrated that samples after sub- and super- critical oxidation were less inhibitory than the stock solution.