The diploma thesis focuses on the monitoring of water quality in the Zemplín Šírava Lake. Field research and sampling took place in spring and autumn months of 2017, 2018 at 6 locations. We measured such physical and chemical indicators as water pH, temperature, conductivity and soluble substances directly on the field. Through cultivation methods, we detected the presence of hygienically important bacterial species such as enterococci, coliform bacteria, thermotolerant coliform bacteria, cultured bacteria at 22 °C. For rapid and accurate identification of bacteria at species level, mass spectrometry was used. The result of MALDI TOF analysis is the presence of the pathogenic bacterium Enterococcus faecalis. On the basis of selected physicochemical and microbiological indicators water quality control was carried out according to Act No. 269/2010 Coll. and Directive 2000/60/EC. By the use of microscopic analysis, we detected the presence of algae and cyanobacteria in water samples. In the Zemplín Šírava Lake, we recorded the presence of the diatoms, which were represented mainly by the species Aulacoseira granulata, Fragilaria crotonensis and several species of Euglena type. The species of Aphanizomenon flos-aquae, Microcystis aeruginosa dominated most of the Cyanobacteria taxa with the ability to form the water flowering. The aim of the research was to thoroughly analyze and assess the quality of water in the Zemplín Šírava Lake and its possible risks to human health. The results of all analyzes confirm the overall satisfactory hygienic status of the Zemplín Šírava Lake.