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Bubble emission mechanisms from submerged Large Igneous Provinces (LIPs) remains enigmatic. The Kerguelen Plateau, a LIP in the southern Indian Ocean, has a long‐sustained history of active volcanism and glacial/interglacial cycles of sedimentation, both of which may cause seafloor bubble production. We present the results of hydroacoustic flare observations around the under‐explored volcanically‐active Heard Island and McDonald Islands on the Central Kerguelen Plateau. Flares were observed with a split‐beam echosounder and characterized using multi‐frequency decibel differencing. Deep‐tow camera footage, water properties, water‐column δ3He, sub‐bottom profile, and sediment δ13C and δ34S data were analyzed to consider flare mechanisms. Excess δ3He near McDonald Islands seeps, indicating mantle‐derived input, suggests proximal hydrothermal activity; McDonald Islands flares may thus indicate CO2, methane, and other minor gas bubbles associated with shallow diffuse hydrothermal venting. The Heard Island seep environment, with sub‐bottom acoustic blanking in thick sediment, muted 3He signal, and δ13C and δ34S fractionation factors, suggest Heard seeps may either be methane gas (possibly both shallow biogenic methane and deeper‐sourced thermogenic methane related to geothermal heat from onshore volcanism) or a combination of methane and CO2, such as seen in sediment‐hosted geothermal systems (Procesi et al., 2019). These data provide the first evidence of submarine gas escape on the Central Kerguelen Plateau and expand our understanding of seafloor processes and carbon cycling in the data‐poor southern Indian Ocean. Extensive sedimentation of the Kerguelen Plateau and additional zones of submarine volcanic activity mean additional seeps or vents may lie outside the small survey area proximal to the islands. Science Foundation Ireland Australian Antarctic Science Program Australian Research Council Australian Government