Water column hypoxia, low tissue pO2 and H2S intrusion, a known phytotoxin, are linked to global seagrass decline. While many lab experiments have examined these relationships, only field studies capture the complexity of gas dynamics in situ. We examined internal pO2 and H2S dynamics in a dominant tropical seagrass Thalassia testudinum using microsensors. Based on 12 field deployments (48–72-h) across seasons, we show that T. testudinum has a high capacity for daytime leaf oxidation (42–53 kPa) that sustains oxic conditions in its tissues and supersaturates the water column with O2 (>21 kPa). While internal daytime O2 is consumed near sunset, positive feedback between seagrass O2 production and the supersaturated water column going into the night contributes to buffering of internal plant hypoxia at the beginning of the night. Leaf meristems went anoxic/hypoxic (0.6 kPa) at night even with high daytime irradiance, indicating a high ecosystem O2 consumption, and reliance on water column pO2 (19 kPa) through leaf pO2 (9 kPa) to prevent H2S from entering the meristem at night. Newly recruiting shoots into bare sediment also had the ability to minimize H2S intrusion. At ambient irradiance, we only detected H2S in the meristem when water column pO2 was hypoxic (<2 kPa) coincident with maximum water column temperatures (33 oC), an occurrence likely to increase with global warming. These data reinforce the importance of water quality management to sustain seagrass-dominated systems, particularly in nutrient-enriched estuaries and coastal lagoons.