Three different kinds of water treatment and two configuration modes were applied to examine the biochemical and physiological responses of P. stenoptera and T. ascendens saplings under simulated vegetation of the Hydro-fluctuation Belt of the Three Gorges Reservoir Region. The water treatments were normal growth water condition ( CK), light drought water stress (LD) and water submersion (SM). The first configuration mode was 3 P. stenoptera and 6 T. ascendens, and the second was a reverse of the number of saplings of both species. The results showed that different configuration modes could not significantly influence the photosynthetic pigment, SOD, POD, CAT, ASP, O2·—, proline and soluble protein of the two species. In contrast, different water treatment and time had significant influences on SOD, POD, CAT, ASP, O2·— and soluble protein of the two species. The interaction of configuration modes x water treatment, configuration modes x time, configuration modes x water treatment x time had no significant influence on photosynthetic pigment, SOD, POD, CAT, ASP, O2·— and soluble protein of the two species. However, the interaction of water treatment x time had significant influences on SOD, POD, ASP and O2·— of P. stenoptera, as well as on SOD, CAT, ASP and proline content of T. ascendens.Our study showed that both species had to some extent different biochemical and physiological responses to water stress, and were relatively well-adapted to the dynamic hydrological environment in the hydro-fluctuation belt of the Three Gorges Reservoir Region.