Algal blooms, resulting from the overgrowth of algal plankton in water bodies, pose significant environmental problems and necessitate effective remote sensing methods for monitoring. In recent years, Global Navigation Satellite System–Reflectometry (GNSS-R) has rapidly advanced and made notable contributions to many surface observation fields, providing new means for identifying algal blooms. Additionally, meteorological parameters such as temperature and wind speed, key factors in the occurrence of algal blooms, can aid in their identification. This paper utilized Cyclone GNSS (CYGNSS) data, Sentinel-3 OLCI data, and ECMWF Re-Analysis-5 meteorological data to retrieve Chlorophyll-a values. Machine learning algorithms were then employed to classify algal blooms for early warning based on Chlorophyll-a concentration. Experiments and validations were conducted from May 2023 to September 2023 in the Hongze Lake region of China. The results indicate that classification and early warning of algal blooms based on CYGNSS data produced reliable results. The ability of CYGNSS data to accurately reflect the severity of algal blooms opens new avenues for environmental monitoring and management.