SummarySeagrass is constantly challenged with transporting sufficient O2from above‐ to belowground tissue via aerenchyma in order to maintain aerobic metabolism and provide protection against phytotoxins.Electrochemical microsensors were used in combination with a custom‐made experimental chamber to analyse the belowground biogeochemical microenvironment ofZostera muelleriunder changing environmental conditions.Measurements revealed high radial O2release of up to 500 nmol O2 cm−2 h−1from the base of the leaf sheath, maintaining ac. 300‐μm‐wide plant‐mediated oxic microzone and thus protecting the vital meristematic regions of the rhizome from reduced phytotoxic metabolites such as hydrogen sulphide (H2S). H2S intrusion was prevented through passive diffusion of O2to belowground tissue from leaf photosynthesis in light, as well as from the surrounding water column into the flow‐exposed plant parts during darkness. Under water column hypoxia, high belowground H2S concentrations at the tissue surface correlated with the inability to sustain the protecting oxic microshield around the meristematic regions of the rhizome. We also found increased pHlevels in the immediate rhizosphere ofZ. muelleri, which may contribute to further detoxification of H2S through shifts in the chemical speciation of sulphide.Zostera muellerican modify the geochemical conditions in its immediate rhizosphere, thereby reducing its exposure to H2S.