In the present study, water samples from 8 sites known as: Taploca, Nagy-borvíz, Piricske (located in Romania) and Szent Jakab, Kiskút, Kossuth Lajos, Polányi kút and Berzsenyi (located in Balaton highland in Hungary) and characterized with low nutrient content, were studied using cultivation independent methods. Diversity indices and cell counts were determined to assess the species richness in relation to the cell counts within the samples. Next generation sequencing was used to reveal the

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... sting microbial community, and taxon specific PCR was used to detect the presence of some species with hygienic. 18 bacterial phyla above a ratio of 2% were identified in addition to 13 archaeal phyla using amplicon sequencing. Nagy-borvíz water sample showed a unique presence of Chloroflexi, Bacteroidota, Desulfobacterota, Acidobacteriota and Actinobacteriota. Piricske water sample showed mostly Caldisericota and Spirochaetota. Taploca water sample contained a unique presence of Planctomycetota and Myxococcota at the same time with Szent Jakab water sample which showed an additional presence of Chloroflexi, Berzsenyi contained Campylobacterota at the same time with Polányi kút which had important fractions of Nitrospirota and Desulfobacterota. Finally, Kossuth Lajos water sample was dominated by Fusobacteriota, mainly members of Hypnocyclicus genus. Piricske and especially Nagy-borvíz water samples contained important fractions of Altiarchaeota, moreover, Piricske contained high fraction of Euryarchaeota phylum -most of them belong to Methanobacteriaceae family. Nitrosopumilaceae dominated Taploca and Kiskút in addition to their important presence in the rest of the samples. Diversity indices and cell count showed in general that cell count values are tending to be lower when the diversity is higher. The results of taxon specific PCR reactions showed that water treatment would be essential in some water samples.