This work is based on the current issue of increasing concentrations of pharmaceutical residues in various components of the environment. These new environmental contaminants continuously enter the environment. The most affected environmental component is the aquatic environment. This study is focused on the development and optimization of reliable analytical method, which can determine selected drugs in the aquatic environment (waste waters and surface waters) qualitatively and quantitatively. The target compounds were selected mainly from the group of non-steroidal anti-inflammatory drugs (NSAID): salicylic acid, acetylsalicylic acid, clofibric acid, ibuprofen, acetaminophen, caffeine, naproxen, mefenamic acid, ketoprofen and diclofenac. NSAIDs are one of the most used drugs in Czech Republic. For the final analysis of this study was used the comprehensive two-dimensional gas chromatography with mass spectrometric detection Time-of-Flight (GCxGC-TOF MS). It is a very sensitive and reliable analytical method for trace and ultra-trace analysis. Simultaneously, solid phase extraction (SPE) and derivatization are optimized in this work. Optimized analytical method including SPE, derivatization with MSTFA (N-methyl-N-(trimethylsilyl) trifluoroacetamide) and final analysis by GCxGC-TOF MS were applied successfully for the analysis of real samples. Samples of waste water were collected from the waste water treatment plant in Brno – Modřice and samples of surface water were collected from two river streams Svratka and Svitava in Moravian region. The range of concentrations of selected drug residues varied from one to tens of g/L in wastewater and from tens to hundreds of ng/L in surface waters. The degree of wastewater and surface waters contamination by drug residues is assessed in conclusions of the work. Simultaneously, spontaneous degradation of selected drugs in water and removal efficiency of the wastewater treatment plant is assessed in conclusions of the work. The developed method is usable for monitoring and environmental analysis of water ecosystems. It is usable not only for selected drugs, but even for other organic compounds with similar properties.