The research was carried out in Lake Piecki and Lake Nawionek, two lobelia lakes located within the Zaborski Landscape Park. Water samples were collected from the surface and bottom water layers in spring, summer and autumn 2009. The analysis reveals that the total number of planktonic bacteria (TNB) in Lake Nawionek ranged between 8.83 and 36.22·10⁵ cells/cm³ and between 15.77 and 44.93·10⁵ cells/cm³ in Lake Piecki. The highest counts of bacteria were noted in spring. In a majority of tests heterotrophic psychrophilic bacteria (CFU 22℃) were more abundant in the surface water layer while heterotrophic mesophilic bacteria were always more abundant in the bottom water layer. Rods were prevailing morphological forms in both lakes, followed by pleomorphic forms, whereas cocci and bacilli constituted the least abundant microbial groups. Furthermore, ammonifying and nitrifying bacteria were the most common physiological forms in both lakes. Higher physiological activities of bacterial strains were observed in Lake Piecki with the exception of pectinolytic and ureolytic bacteria, which were more active in Lake Nawionek.