Underwater disturbances are the largest error source in GNSS-A seafloor geodetic observation. In particular, the gradient of sound speed structure directly affects the horizontal accuracy and needs to be examined. Previous studies have not investigated its temporal change component. In this paper, we verified the assumption that the underwater gradient structure does not change significantly during GNSS-A observation for several hours through applying a modified version of an analysis software called GARPOS to actual data of SGO-A (provided by Japan Coast Guard). Obtained results suggested that this assumption holds at many observation data, and the positioning accuracy becomes better. Some non-improved observation epochs were speculated to be accompanied by structure changes for which this assumption was not valid. It is suggested that the sound speed structure change during observation will be an important research topic in GNSS-A.