Over 2003–2004 a study was conducted to evaluate microbial quality of surface water of the Žitava river, its branches and adjacent wetlands in the Žitavský luh Nature Reserve. This paper characterizes and describes the most significant microbial communities occurring in this specific environment. The presence of coliform bacteria, myxobacteria, actinomycetes and soil microscopic fungi in the plankton and benthos areas of flowing water (the new Žitava river-bed), stagnant water (adjacent old bed of the Žitava) and wetlands. The most numerous communities in the locality under investigation in the area of benthos were coliform bacteria (with the maximum occurrence value of 4.1.104 KTJ. g-1 of benthos) and microscopic fungi (with the maximum occurrence value of 3.5.103 KTJ. g-1 of benthos). From microscopic fungi, species of the genera Aspergillus, Penicillium, Trichoderma, Cladosporium and Fusarium occurred in particular. In the area of wetlands were dominant the species of the genus Trichoderma and in the Žitava river (both new and old river-beds) the species of the genera Penicillium and Aspergillus.