The fate of thawing permafrost carbon is essential for understanding the permafrost–climate feedback and projections of future climate. Here we study transport of organic carbon by groundwater in the active layer of a hillslope model. We find that carbon transport velocities and microbial mineralization rates are strongly dependent on liquid saturation in the seasonally thawed active layer. In a warming climate, the rate at which permafrost thaws determines how fast carbon can be transported.