The safety of beachgoers and swimmers is determined by the presence or absence of microbial contaminants and cyanobacterial toxins in the water. This study compared the assessment of bathing waters according to the Bathing Water Directive, which is based on the concentration of fecal contaminants, with some modifications, and a new method based on the concentration of chlorophyll-a, which corresponds to the World Health Organization (WHO) guidelines used for determining cyanobacterial density in the water posing threat to people health. The results obtained from the method based on chlorophyll-a concentration clearly showed that the number of bathing waters in Poland with sufficient and insufficient quality were higher in 2018 and 2019, compared to the method based on microbial contamination. The closing of bathing waters based only on the visual confirmation of cyanobacterial blooms might not be enough to prevent the threat to swimmers’ health. The multivariate analyses applied in this study seem to confirm that chlorophyll-a concentration with associated cyanobacterial density might serve as an additional parameter for assessing the quality of bathing waters, and in the case of small water reservoirs, might indirectly inform about the conditions and changes in water ecosystems.