A new analytical method for the determination of naproxen, ketoprofen, diclofenac, carbamazepine, and triclosan (TCS) in water samples by liquid chromatography is developed and validated. The method is based on the extraction of the analytes by a polydimethylsiloxane (PDMS) rod. The different parameters affecting extraction, such as the addition of salt, pH, initial volume, extraction and elution times and elution solvent, as well as the application of sonication, are studied. The results showed that the detection limits are all in the 0.1–0.3 µg L−1 range except for carbamazepine (6 µg L−1) with relative standard deviations in the range of 0.4%–9.7%. The method developed, which was validated by analysing spiked surface water samples at 10, 25 and 75 µg L−1 gave recoveries of between 84.8% and 111.2%. In the case of carbamazepine, a recovery of 99.1% was obtained at 75 µg L−1. The main advantage of the developed method is that allows high performance liquid chromatography–diode array detection, which is widely available in non-specialised laboratories, to be applied for pharmaceuticals and TCS determination in surface waters after performing a preconcentration/clean-up step with PDMS rods as it has been shown by analysing real water samples.