This study identifies the ecological status of lakes which are significant water bodies located within Polish national and landscape parks. The assessment carried out on the basis of data from the National Environmental Monitoring System coming from 2010-12 took into account the requirements of the Water Framework Directive (WFD). Half of the lakes analyzed were characterized by at least good status, while the others were in moderate or even poor or bad status, although they were situated in protected areas. The study shows multi-aspect (morphometric, hydrological, and catchment-related) factors that determine the water quality and the status of the lake ecosystem. A strong correlation was found between eutrophication indicators (chlorophyll a concentration, water transparency, nutrient concentrations in water) and the majority of limnological parameters of lakes. There was no direct relationship between the percentage shares of the major land uses of lake catchments and the ecological status of lakes, but the nitrogen and phosphorus load theoretically emerging in the catchment correlated with the nutrient concentrations in water, as well as with chlorophyll a and water transparency. On the basis of data available, it proved impossible to identify a positive impact of covering lakes with protection within a national or landscape park on their ecological status.