The construction of the Three Gorges–Gezhouba Dam cascade hydropower station has changed the water level fluctuation pattern of the habitats for remnant rare and endangered Myricaria laxiflora populations downstream of the dam. The present study utilized biochemical markers of photosynthetic physiology to evaluate the spatiotemporal responses of remnant populations to human-regulated water level fluctuations. The results showed that the photosynthetic physiological activities of remnant M. laxiflora populations underwent a period of rapid growth, followed by a gradual decline in the growth recovery phase after flooding. During the entire experimental period, photosynthetic physiological activities of remnant M. laxiflora populations changed with prolongation of emergence time: specifically, net photosynthetic rate and stomatal conductance initially decreased and then subsequently increased, intercellular carbon dioxide concentrations peaked at mid-phase and transpiration rate continuously increased. The maximum net photosynthetic rate, apparent photosynthetic quantum efficiency and dark respiration rate in the light–response curves of the plants continuously increased during growth. The water level gradient also significantly affected the photosynthetic physiological activities in the remnant populations, i.e. the photosynthetic physiological activities of high-altitude plants were significantly higher than the middle- and low-altitude plants. The changes in photosynthetic pigment content of plants in remnant populations during the growth recovery phase and the entire growth period were similar to those occurring in photosynthetic activities in plants. Further, canonical correspondence analysis showed that photosynthetic physiological activities in the plants were significantly correlated with changes in water levels, emergence time, elevation gradient, soil water and soil nitrogen contents. Therefore, the artificial regulation of water level fluctuations by large hydropower stations will inevitably affect the photosynthetic activities and growth of remnant M. laxiflora populations.