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Abstract Bubble emission mechanisms from submerged large igneous provinces remains enigmatic. The Kerguelen Plateau, a large igneous province 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 underexplored volcanically active Heard Island and McDonald Islands on the Central Kerguelen Plateau. Flares were observed with a split‐beam echosounder and characterized using multifrequency decibel differencing. Deep‐tow camera footage, water properties, water column δ3He, subbottom 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 subbottom acoustic blanking in thick sediment, muted 3He signal, and δ13C and δ34S fractionation factors, suggest that Heard Island 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. 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.