© 2014 New Phytologist Trust. Seagrass is constantly challenged with transporting sufficient O2 from 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 of Zostera muelleri under changing environmental conditions. Measurements revealed high radial O2 release of up to 500 nmol O2 cm-2 h-1 from the base of the leaf sheath, maintaining a c. 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 O2 to 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 pH levels in the immediate rhizosphere of Z. muelleri, which may contribute to further detoxification of H2S through shifts in the chemical speciation of sulphide. Zostera muelleri can modify the geochemical conditions in its immediate rhizosphere, thereby reducing its exposure to H2S.