This study investigates eutrophication in Kraków’s urban freshwater bodies by analysing chlorophyll-α concentrations, which indicate phytoplankton biomass. We measured chlorophyll-α 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-α levels, suggesting resistance to significant phytoplankton blooms. In contrast, Zalew Nowohucki exhibited notable chlorophyll-α fluctuations and peaks, indicating variable conditions and nutrient inputs. The pond in Park Lotników and Staw Dąbski also displayed variability with rapid chlorophyll-α peaks, indicating increased susceptibility to eutrophication. Cyanobacteria content varied, 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.