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The Wagner basin, located in the northernmost Gulf of California, hosts a large reservoir with geothermal potential documented in recent heat flow surveys. Although there is evidence of heat generation above the average value for an oceanic crust in the Wagner basin, it is unclear what the heat source is. To better understand the thermal structure in the northern Gulf of California, we acquired four 2D multichannel seismic reflection profiles and two systematic heat flow profiles across the Wagner basin. The survey targeted a geothermal anomaly, which we denominated “Devil's Hole” in a clear reference to pockmarks on the seafloor, and very high heat flow values. The heat flow profiles are ∼12 and ∼9 km long, are sub perpendicular to each other, have a nominal measurement spacing of ∼1 km, and were located along the transects of two of the four seismic reflection profiles. The two remaining seismic profiles are ∼34 and ∼40 km long, respectively, and are oriented SWW-NEE. To obtain seismic images, we used a conventional seismic processing workflow. After heat flow data correction, the minimum, maximum, and standard deviation of heat flow values for the Wagner basin are 295±42 and 10,894±114 mW/m2. We interpret the relatively high heat flow and large variability in the central part of the acquired profiles is caused by upward fluid flow at the Wagner fault zone. In contrast, the lower heat flow in the western flank of the basin suggest conductive heat transfer given the absence of faults. Based on these observations, we develop a geological model in which venting is not the product of a nascent spreading center as other authors have suggested. Instead, hydrothermal activity appears to result from isolated thermal plumes, rising from the base of the sedimentary column, captured by permeable fracture systems.