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Abstract Background The permeability of plasma membrane aquaporins (PIPs) to small solutes other than water greatly diversifies their potential functions in plant development and metabolic processes. One such process is stress signalling in which hydrogen peroxide (H2O2) plays a major role. Based on transport assays carried out in yeast, there are differences in the degree to which PIPs of Arabidopsis thaliana, are permeable to H2O2 and thus they may differentially facilitate transmembrane diffusion. Here, we test whether specific PIPs aid in the transmembrane diffusion of H2O2 to such an extent that knocking-out PIPs affects plant phenotype. We examined changes in growth and morphology, including biomass accumulation, root system architecture and relative water content, as well as gas exchange, across two H2O2 treatments in knockout mutants of A. thaliana. Results We could infer that PIP-type aquaporins are permeable to H2O2 in planta and that this permeability is physiologically relevant in a plant’s response to oxidative stress. In particular, the lack of functional PIP2;3 confers resistance to exogenously applied H2O2 indicating that it facilitates H2O2 entry into root cells. Additionally, PIP1;1 and PIP2;6 were found to facilitate H2O2 diffusion, while PIP2;2 is required for proper root growth under controlled conditions. Main findings We conclude that PIPs are physiologically relevant conduits for H2O2 diffusion in the A. thaliana roots and participate in the regulation of stress responses.