Abstract: Comprehensive understanding of the current state of water body eutrophication is crucial for long-term water environmental management. However, there have been few reports on the analysis of the spatiotemporal variations and causes of pollution in seasonal rivers with regards to eutrophication. Based on monitoring data of 13 water quality indicators in the Meishan section of the Minjiang River Basin from January 2019 to December 2020, this study used eutrophication indices, Geographic Information Systems (GIS) technology, and multivariate statistical methods to elucidate the spatial and temporal characteristics of nutrient salts, the state of eutrophication, and the main polluting factors of the main stem and major tributaries of Minjiang River in the basin. The results indicated that: (1) Temporally, total nitrogen (TN) concentrations were highest in summer, reaching 5.33 mg/L. Total phosphorus (TP) and ammonia nitrogen (NH3-N) were highest in spring, at 0.22 and 0.65 mg/L, respectively. Spatially, TN concentrations were highest in the Simeng River, reaching 7.09 mg/L. TP and NH3-N concentrations were highest in the Tiquan River, at 0.27 and 0.96 mg/L, respectively; (2) The eutrophication index ranked as follows: spring (69.10) > summer (67.06) > winter (65.93) > autumn (65.91); Tiquan River (76.06) > Simeng River (70.39) > Mao River (70.02) > Jinniu River (63.14) > main stem of the Minjiang River (62.19); (3) Principal component analysis extracted 4 principal components, cumulatively explaining 71.11% of the variance, identifying the primary factors influencing water quality were industrial and domestic wastewater, agricultural activities and urban non-point source pollution, seasonal factors, and soil erosion. The results of this study provided guidance for eutrophication control and water quality improvement in the Meishan section of the Minjiang River Basin and provided a scientific basis for the management of water environment in similar seasonal rivers.