Our study aims to investigate the water quality and distribution patterns of phytoplankton communities in the Jinjiang River Basin in Quanzhou, as well as their relationship with environmental factors. We integrated data from the national water quality databases of the two main tributaries of the West and East Jinjiang Rivers between 2020 and 2023, supplemented by field surveys. Redundancy analysis was used to explore the effect of environmental factors on phytoplankton communities. Our findings revealed that the West Jinjiang River experienced a significant influence from excessive fertilizer use in tea cultivation, leading to an increase in TN concentrations compared to the East Jinjiang River. The abundance of phytoplankton in the Jinjiang River Basin was 105 cells·L−1, with phytoplankton being dominated by Chlorophyta, Cyanphyta, and diatoms, accounting for an average of 50%, 20%, and 19% of the total phytoplankton abundance, respectively. Redundancy analysis indicated that temperature, pH, and nutrient concentrations were important factors influencing the phytoplankton communities. With increasing temperature and nutrients concentrations, the abundance of Chlorophyta and Dinophyta significantly increased. This study provides a solid foundation for the regular “health diagnosis” of crucial rivers and lakes in Quanzhou and supports the establishment of a health guarantee system for rivers and lakes.