Research on ecophysiology of benthic bacteria indicates that microbiological processes which occur in bottom sediments have a major influence on the development of water bodies. Organic matter accumulated on the bottom makes lakes shallower and accelerates their aging. Microbiological processes are particularly important in small lakes, which are a common element of the environment. This article presents the results of the investigation of the distribution of heterotrophic bacteria in the bottom sediments of four lakes with different trophic conditions in the Bory Tucholskie National Park and the relationship between the number of benthic bacteria and their physiological activity. The total number of benthic bacteria and the ability of isolated strains to carry out selected physiological processes were assessed by cultivating bacteria on appropriate substrates. We also determined the coefficient of physiological activity, which was then used for the correlation analysis and verification of the research hypothesis. The highest number of benthic bacteria was found in the eutrophic and dystrophic lakes. The lowest number was recorded in lake sediments of the mesotrophic lake, although at this site the studied strains were the most active. As a result, the correlation analysis confirmed the hypothesis that there is no relationship between the metabolic potential of benthic bacteria and their number in a sample.