Fresh submarine groundwater discharge (FSGD), a well-established land-to-sea pathway for water and materials, has increased (∼30%) along the midlatitude coast of Japan with the shift from snowfall to rainfall since the 1980s. The terrestrial-derived FSGD in this area has a residence time of 10-20 years, and its material flux may respond quickly to the effects of recent warming. In this study, FSGD collected directly from the seafloor (∼10 m water depth) during two different periods (2017-2021 and 2001-2003) was observed using the same consistent method to evaluate the warming-related effects on FSGD material fluxes. In the FSGD system, dissolved constituents and the isotopic composition decreased by 10-30% and residence time by one-third compared to the previous data, even though homogeneous water quality was maintained among the FSGD-connected aquifers for each period. Most concerning is that these changes resulted in a drop in pH and an increase in FSGD-derived carbon flux. Total nutrient fluxes from land have roughly halved, resulting in lower primary productivity and an estimated doubling of excess dissolved inorganic carbon in coastal waters. Our findings present direct evidence of the sensitivity of carbon flux to climate change and the urgency for carbon-related FSGD research worldwide.