Fresh Submarine Groundwater Discharge (FSGD) is an important pathway for the transport of water and materials from land to ocean, but changes in the transport may occur as snowfall decreases. This study was conducted on Japan’s mid-latitude western coast where FSDG is a quarter of the total riverine discharge and snowfall has decreased by ~50% since the 1990s. The altitude of the FSGD recharge area in 2018 has shifted 100–150 m higher than that in 2000, and the water residence time has decreased from 4-15 to 3-11 years. The pH of the groundwater dropped by 0.5, its CO (aq) concentration doubled, and nitrogen and phosphorus decreased by 30–40% and 70–80%, respectively. These changes in nutrients reduced primary productivity in coastal waters and doubled the excess dissolved inorganic carbon flux. Our evidence highlights the sensitivity of FSGD carbon flux to climate change and of the urgency of carbon-related FSGD research worldwide.