Water quality in the dam Ružín is mainly affected by the mining operations together with acid and metalliferous drainage (AMD) and occurrence of heavy metals in bottom sediments. Absence of public sewer system in several villages situated in the Hornad and Hnilec river basins can be considered a cause of poor hygiene. Culture, microscopic and molecular methods were used to assess the biodiversity of microorganisms in mining-related water. Culture methods were used to determine the occurrence of important hygiene-related bacteria species (enterococcus, coliform bacteria, hyperthermophilic coliform bacteria, cultivable at the temperature of 22 °C, iron and manganese bacteria). Water quality was controlled following physical-chemical methods and microbiological indicators according to the Law 364/2004 Z. z., 269/2010 Z. z. and Regulations 2000/60/ES. Bad situation of the dam Ruzin is proven by overstepped limits of physical-chemical as well as biological indicators. The outcome of the analysis MALDI TOF is to determine the pathogenic bacteria Pseudomonas sp. and Comomonas sp. The occurrence of cyanobacteria species, algae and iron bacteria was investigated using microscopic methods. The occurrence of the class of diatom Bacillariophyta was observed in all habitats. Major cyanobacteria species observed were as follows: Microcystis aeruginosa, Woronichinia neageliana a Aphanizomenon flos-aque. The occurrence of iron bacteria Leptotrix sp. a Galionella sp. as an indicator of neutral mining-related water was confirmed as well. Poor hygiene of the dam Ruzin is confirmed by the outcomes of analyses.