We examine the thermal effects of seamount subduction. Seamount subduction may cause transient changes in oceanic crust hydrogeology and plate boundary fault position. Prior to subduction, seamounts provide high-permeability pathways between the basaltic crustal aquifer and overlying ocean that can focus fluid flow and efficiently cool the oceanic crust. As the seamount is subducted, the high-permeability pathway is closed, shutting down the advective transfer of heat. If significant fluid flow occurs, it would be restricted after seamount subduction and would result in a redistribution of heat warming the trench and cooling landward parts of the system. Additionally, subducting seamounts can influence the position of the plate boundary fault that has thermal consequences by locally controlling the proportions of incoming sediment that subduct and accrete. Shifting the décollement to the seafloor at the trench in the wake of seamount subduction causes limited cooling focused at the toe of the margin wedge. We apply these features of seamount subduction to a thermal model for the Nankai Trough Seismogenic Zone Experiment transect on the margin of Japan. Models with hydrothermal circulation provide an explanation for anomalously high surface heat flux observations near the trench. They yield temperatures of ∼100°C−295°C for the rupture area of the 1944 Tonankai earthquake. Temperatures in the region of episodic tremor and slip are estimated at ∼290°C–325°C, ∼70°C cooler than a model with no fluid circulation.