We characterized the short-term response to waterlogging in Quercus petraea (Matt.) Liebl. and Quercus robur L. as the initial response towards their known long-term differences in tolerance to waterlogging. One-month old seedlings were subjected to hypoxic stress and leaf gas exchange, shoot water potential (Psi(s)) and root hydraulic conductivity (Lp(r)) were measured. In parallel, the expression of nine aquaporins (AQPs) along the primary root was analysed by quantitative RT-PCR. Results showed a similar reduction in net assimilation (A) and stomatal conductance (g(s)) for the two species. Notably, the response of Lpr differed temporally between the two species. Q. robur seedlings exhibited a significant early decline of Lpr within the first 5 h that returned to control levels after 48 h, whereas Q. petraea seedlings showed a delayed response with a significant decrease of Lp(r) exhibited only after 48 h. Transcriptional profiling revealed that three genes (PIP1;3, TIP2;1 and TIP2;2) were differentially regulated under stress conditions in the two oak species. Taken together, these results suggested species-specific responses to short-term waterlogging in terms of root water transport.