There is growing public health concern about the development of antimicrobial strains of bacteria and the possibility that the continuous exposure of natural microbes to antibiotic residues in the environment could be one pathway. For a complete perspective on fate and transport of antibiotics in the aquatic environment and their potential role in this process, both aqueous phase and sediment concentrations are important to determine environmental exposure. Sulfamethoxazole (SMX), trimethoprim (TMP), ciprofloxacin (CPX), and tetracycline (TCC) were quantified in surface water and sediment extracts using standard addition and isotopically labeled surrogates. While SMX was found at the highest concentrations in surface waters (198–328 ng/L), CPX was the most concentrated in the sediments (20–25 ng/g). An alternative fate for aqueous phase antibiotics is that of photolysis. To evaluate this process under laboratory conditions, a reactor was constructed to simulate a controlled stream environment. SMX was shown to degrade in the presence of UV-light into sulfanilic acid and a photoisomer. Highly organic sediments were the most efficient at removing SMX from the aqueous phase.