In recent times, there has been increasing discussion about the harmful effects of certain pharmaceuticals, in other words antibiotics, on the environment, but also on human health. At present, there is no law forbidding or decreasing their use. In fact, their use is increasing year by year and the increase is almost impossible to stop. In this paper, methods of sample preparation are developed for analysis of thirteen pharmaceutically active compounds (albendazole, azithromycin, etodolac, febantel, imatinib, levamisole, linezolid, omeprazole, praziquantel, sulfafurazole, sulfamethazine, tiamulin, torasemide) in water and sediment samples – stir bar sorptive extraction and ultrasound extraction. In order to determine optimal conditions for stir bar sorptive extraction, pure organic solvents were used at different pH values of water, with differing volumes of solvents for desorption, at differing time intervals of extraction and desorption, as well as at differing temperatures of extraction. Ultrasound extraction was done by using pure organic solvents (and their mixtures) and mixtures of solvents with acids and bases. It was thenceforth determined that for optimal conditions of extraction of pharmaceuticals from water (stir bar sorptive extraction) pure organic solvent, methanol, volume 5 mL at extraction and desorption temperatures of 30°C and water pH value of 3.0 is best used. Furthermore, for optimal extraction conditions of pharmaceuticals from sediments using ultrasound extraction, a pure organic solvent, methanol, volume 10 mL, at extraction temperature of 25 °C was chosen. The efficacy of extraction was quantitatively determined by ultra high-performance liquid chromatography. After the optimization process, the method was validated and applied to real samples.