Arctic and subarctic watersheds are undergoing climate warming, permafrost thawing, and thermokarst formation resulting in quantitative shifts in surface water –groundwater interaction at the basin scale. Groundwater currently comprises almost one fourth of Yukon River water discharged to the Bering Sea and contributes 5–10% of the dissolved organic carbon (DOC) and nitrogen (DON) and 35–45% of the dissolved inorganic carbon (DIC) and nitrogen (DIN) loads. Long-term streamflow records (>30 yrs) of the Yukon River basin indicate a general upward trend in groundwater contribution to streamflow of 0.7–0.9%/yr and no pervasive change in annual flow. We propose that the increases in groundwater contributions were caused predominately by climate warming and permafrost thawing that enhances infiltration and supports deeper flowpaths. The increased groundwater fraction may result in decreased DOC and DON and increased DIC and DIN export when annual flow remains unchanged.