This study investigates eutrophication in Kraków’s urban freshwater bodies by analysing chlorophyll-a concentrations, which indicate phytoplankton biomass. We measured chlorophyll-a using fluorescence in four lakes: Staw Płaszowski, Zalew Nowohucki, the pond in Park Lotników, and Staw Dąbski and applied the Trophic State Index (TSI) to evaluate their eutrophication levels. Staw Płaszowski showed stable, low chlorophyll-a levels, suggesting resistance to significant phytoplankton blooms. In contrast, Zalew Nowohucki exhibited notable chlorophyll fluctuations and peaks, indicating variable conditions and nutrient inputs. The pond in Park Lotników and Staw Dąbski also displayed variability with rapid chlorophyll peaks, indicating increased susceptibility to eutrophication. Cyanobacteria content varied, with Zalew Nowohucki showing the highest variability and the pond in Park Lotników having a high proportion of cyanobacteria, likely due to its early stage of development. No cyanobacterial blooms reached critical levels. TSI classifications were: Staw Płaszowski as mesotrophic, Zalew Nowohucki as eutrophic, and the pond in Park Lotników as mesotrophic. Staw Dąbski showed seasonal fluctuations between mesotrophic and eutrophic states. Effective management requires a comprehensive approach, integrating multiple environmental factors and extensive sampling. Future research should focus on long-term monitoring and broader watershed considerations, including urban lakes, for effective eutrophication management.