A primary control on the geodynamics of rifting is the thermal regime. To better understand the geodynamics of rifting in the northern Gulf of California we systematically measured heat-flow across the Wagner Basin, a tectonically active basin that lies near the southern terminus of the Cerro Prieto fault. The heat flow profile is 40 km long, has a nominal measurement spacing of ~ 1 km, and is collocated with a seismic reflection profile. Heat flow measurements were made with a 6.5-m violin-bow probe. Although heat flow data were collected in shallow water, where there are significant temporal variations in bottom water temperature, we use CTD data collected over many years to correct our measurements to yield accurate values of heat flow. After correction for bottom water temperature, the mean and standard deviation of heat flow across the western, central, and eastern parts of the basin are 220±60, 99±14, 889 ± 419 mW m-2, respectively. Corrections for sedimentation would increase measured heat flow across the central part of basin by 40 to 60%. We interpret the relatively high heat flow and large variability on the western and eastern flanks in terms of upward fluid flow at depth below the seafloor, whereas the lower and more consistent values across the central part of the basin are suggestive of conductive heat transfer. Moreover, heat flow across the central basin is consistent with gabbroic underplating at a depth of 15 km and suggests that continental rupture here has not gone to completion.