The effects of flooding on rhizospheric organic acid concentrations of three abundant flooding tolerant plant species (Alternanthera philoxeroides Mart., Arundinella anomala Steud., Salix variegata Franch.) from the water fluctuation zone of the Three Gorges Reservoir (TGR, Yangtze River) were investigated. Soil solution samples of eight low molecular weight organic acids were obtained from rhizotrons using micro suction cups during 3 weeks of waterlogging, after 6 weeks flooding and after a 1 week recovery. To estimate the contribution of water temperature and microbial community, plants in sterile glass bead substrate and original Yangtze sediment were submerged in laboratory at +10°, +20° and +30°C. Waterlogged plants did seldom express a significantly different pattern of rhizospheric organic acid (OA) composition compared to control plants. Flooding caused no burst of organic acid concentration in soil solution: All species express a silencing strategy. Average OA levels were higher in A. anomala rhizosphere than in the other two species, but increased again after resurfacing in all species. Temperature had a stronger influence in sediment than in sterile setup. In contrast to field measurements, succinate, malate and citrate were detected in the sterile setup. Microbial contribution appeared to have great influence on increasing OA occurrence.