Heat flow measurements were conducted at four sites in the Nankai accretionary prism southeast of the Kii Peninsula, around the area where the megasplay fault reaches the surface, in conjunction with long-term monitoring of bottom water temperature at nearby stations. Analysis of the obtained data showed that variations in bottom water temperature seriously affect surface heat flow measurements in the areas with water depths of less than about 2,800 m. This effect can reach up to 20% to 30% and may have significantly contributed to a large scatter in the heat flow values previously measured in the study area. The temperature records were also used to determine heat flows from sediment temperature profiles disturbed by bottom water temperature variations. Results of measurements at sites deeper than 2,800 m indicate that the regional heat flow, corrected for surface disturbances including the influence of bathymetric relief, is about 65 mW/m2, which is consistent with the value calculated using subduction thermal models. Local high heat flow values were obtained in the vicinity of the tips of the branches of the splay fault, suggesting advective heat transport by upward pore fluid flow along the faults.