We studied the seismic attenuation of body waves in the south‐central region of the Gulf of California (GoC) with records from the Network of Autonomously Recording Seismographs of Baja California (NARS‐Baja), from the Centro de Investigación Científica y de Educación Superior de Ensenada’s Broadband Seismological Network of the GoC (RESBAN), and from the ocean‐bottom seismographs (OBS) deployed as part of the Sea of Cortez Ocean Bottom Array experiment (SCOOBA). We examine 27 well‐located earthquakes reported in Sumy et al. (2013) that occurred from October 2005 to October 2006 with magnitudes (Mw) between 3.5 and 4.8. We estimated S‐wave site effects by calculating horizontal‐to‐vertical spectral ratios and determined attenuation functions with a nonparametric model by inverting the observed spectral amplitudes of 21 frequencies between 0.13 and 12.59 Hz for the SCOOBA (OBS) stations and 19 frequencies between 0.16 and 7.94 Hz for NARS‐Baja and RESBAN stations. We calculated the geometrical spreading and the attenuation (1/Q) factors for two distance intervals (10–120 and 120–220 km, respectively) for each frequency considered. The estimates of Q obtained with the SCOOBA (OBS) records for the interval 10–120 km indicate that the P waves attenuate more than S waves (QP=34±1.2f 0.82±0.10, QS=59±1.1f 0.90±0.03) for frequencies between 0.6 and 12.6 Hz; whereas for the 120–220 km interval, where ray paths travel deeper, S waves attenuate more than P waves (QP=117±1.3f 0.44±0.19, QS=51±1.2f 1.12±0.11). The estimates of Q obtained using NARS‐Baja and RESBAN records, within 10–120 km, indicate that P waves attenuate more than S waves (QP=69±1.2f 0.87±0.16, QS=176±1.4f 0.61±0.26) at frequencies between 0.3 and 6.3 Hz; whereas at the 120–220 km distance interval S waves attenuate slightly more than P waves (QP=39±1.1f 0.64±0.06, QS=48±1.1f 0.37±0.07) at high frequencies (f>3 Hz). These results, based on a unique OBS dataset, provide an indirect mean to constrain future models of the thermal structure beneath the GoC.