Abstract: As the largest river in Jiangxi Province, the middle reaches of the Ganjiang River play a crucial role in regional water security and ecological barriers. Based on the water quality monitoring data of 86 points during the normal water period, abundant water period and dry water period in 2023 and 2024, the water quality status was evaluated by Pearson correlation, principal component analysis and comprehensive water quality index method. The spatio-temporal variation characteristics of water quality were comprehensively analyzed, and the biological driving mechanism of water quality changes was explored by combining the periphyton biological integrity index (P-IBI) and the benthic macroinvertebrate biological integrity index (B-IBI). A systematic study was conducted on the water quality of 36 typical rivers in the middle reaches of the Ganjiang River. The results show that: (1) There are significant spatial distribution differences. Organic pollution and nutrient salt indicators are unevenly distributed in the Wujiang River Basin, mainly driven by agricultural non-point source pollution and industrial point source emissions. (2) The seasonal variation pattern is clear. The water quality status shows "dry season > normal water period > flood period". During the flood period, the chemical oxygen demand (COD) and five-day biochemical oxygen demand (BOD5) increase by 17.3% and 29.6% respectively compared with the dry season, mainly driven by the input of non-point source pollutants carried by precipitation runoff; the total nitrogen (TN) and total phosphorus (TP) concentrations are the lowest in the dry season, and the comprehensive water quality index (WQI) results are the best, with significantly higher water quality stability than the flood period, mainly related to natural hydrological processes such as flow velocity and water temperature and seasonal human activities. (3) The biological driving mechanism is obvious. P-IBI is significantly positively correlated with NH3-N and heavy metals, while B-IBI is positively correlated with WQI and pH. The responses of the two to pollution stress are complementary, jointly indicating the self-purification capacity of water bodies. The water quality in the middle reaches of the Ganjiang River is driven by the combined effects of natural hydrological processes and human activities, and it is urgent to implement differentiated management strategies for the basin.