Abstract The super typhoon Hagibis traveled northeastward through eastern Honshu, Japan, causing disastrous heavy rainfalls along its path on October 11 and 12, 2019. We performed a comprehensive space geodetic study of water brought by this typhoon using a dense network of Global Navigation Satellite System (GNSS) receivers in Japan. First, we studied the time evolution of altitude‐corrected precipitable water vapor field and compare the movement of water vapor centroid with the rain distribution from radar rain gauge analyzed precipitation. The total amount of water vapor derived by spatially integrating precipitable water vapor on land remained steady at ∼20 Gt. The total precipitation by this typhoon was ∼92, and ∼33 Gt of it fell onto the land area of eastern Honshu. Next, we studied crustal subsidence caused by the typhoon rainwater as surface load. The GNSS stations located under the typhoon path temporarily subsided 1–2 cm on the landfall day and the subsidence mostly recovered on the next day. Using the vertical crustal movement data, we estimated the distribution of surface water in eastern Honshu assuming the layered spherical earth. The amount of the surface load on October 12 was ∼71 Gt, which significantly exceeds the cumulative rainfall on land. We consider that the excess subsidence largely originates from the selective deployment of GNSS stations in the concave topography, for example, along valleys and within basins, in the mountainous Japanese Islands.