Industrial activities, dam construction, and mining are three human activities important for societal and economic development. However, the effects of these activities on phytoplankton communities have been less quantitatively assessed than those on other groups, such as macroinvertebrates, fish, and periphytic algae. In the present study, we selected the Ganjiang River basin, a tributary of the Yangtze River as the representative area to develop a feasible phytoplankton index of biotic integrity (Phyto-IBI) to evaluate the effects of industrial activities, dam construction, and mining on the biotic integrity of riverine ecosystems. The results showed that the three activities greatly altered the abundance and composition of phytoplankton, with a reduction in phytoplankton species quantity and diversity and an increase in abundance. The health status of the Ganjiang River was fair, and the health statuses of industrial areas, dam areas, mining areas, and reference points were poor, poor, fair, and good, respectively. The three activities damaged the biotic integrity of the aquatic system. Moreover, compared to industrial activities and mining, dam construction is more harmful to aquatic systems in the Ganjiang River. The locally weighted regression scatter plot smoother (LOWESS) method showed that an ammonium nitrogen (NH₃-N) concentration of 0.65 mg L⁻¹ is the environmental protection threshold for planktonic biotic integrity in the Ganjiang River. This study not only quantitatively assesses phytoplankton responses to industrial activities, dam construction, and mining but also provides guidance regarding the ecological monitoring, assessment and protection of riverine ecosystems.