Microbial degradation processes play an important role in chemical water clearance taking place in river sediments. Bacteria remove not only easily degradable organic species, but various xenobiotics as well, producing clear and xenobiotic free water for bank-filtered wells. Atrazine is a widely used herbicide, and it is one of the most common xenobiotics present in Danube water. In this study the pathway and kinetics of atrazine metabolism of sedimental microbiota were studied. Samples were collected from river sediment and from pure microbial growth cultures. An analytical scheme including sample preparation, chromatography and mass spectrometry was developed and optimised. Solid-phase extraction (SPE) was found to be satisfactory for sample preparation. For qualitative analysis of samples both reversed-phase and normal-phase high-performance liquid chromatography/mass spectrometry (HPLC/MS) methods were developed and used. Selectivity, detection limits and accuracy of the two methods were compared. Using this analytical scheme, the full atrazine metabolism of the organism Comamonas acidovorans was explored. Altogether, 12 metabolites were identified from the original compound to the urea end product. Detection limits in the range of 50 ng L(-1)-1 microg L(-1) were obtained for different metabolites.