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The position of an underwater target, as determined by the acoustic positioning system and topographic correlation, shows a discrepancy because of bubbles in the water column. Topographic data were obtained from an autonomous underwater vehicle (AUV) in the shallow methane hydrate–bearing area off Joetsu, Japan. Discrepancy between the two locations increased when bubbles existed between the AUV and the mothership. The positioning error trend reflected the positional relationship between the AUV and the ship that varied east–west with time, suggesting that bubbles play a role in reducing the velocity of acoustic signals in the water mass. A locational relationship that does not interpose bubbles between the underwater target and the mothership is required to obtain reliable positioning information for acoustic measurement.