The Baja California peninsula forms the western margin of the Gulf of California (GC) rift system, which is an active tectonic setting manifested by seismicity and numerous geothermal sites. The present study examines the geochemistry of thermal fluids (major ions and gas species, δ18O-δD, δ13C, 3He/4He) from the southern tip of the peninsula (Los Cabos Block, LCB). Sampling was mostly focused on the coastal thermal manifestations in the towns of Buenavista and El Sargento, but other sites further inland are also included for broadening the scope of the study. The main objectives include: (i) characterize water-rock interactions and other processes controlling the fluid composition, (ii) constrain solute geothermometry estimates through multi-step geochemical modeling, and (iii) discuss the fluid origins in terms of tectonics and regional shear-wave velocity anomalies in the upper lithosphere. The geothermal systems in the area have a tectonic origin and result from fluid circulation along regional faults that penetrate the upper crust through the granitic basement. Mixing between the thermal fluids and seawater at the coast is clearly illustrated through major ions and δ18O-δD relationships. Reconstruction of the pre-mixing chemical compositions indicates a low-salinity fluid at Buenavista (Cl = 104–109 mg L−1) and a saline fluid at El Sargento (Cl = 7169 mg L−1). The geochemical modeling allows us to validate these endmember compositions and to address a common issue when using solute geothermometry, which is the uncertainty on the state of equilibrium of the thermal fluid with respect to wall-rock minerals. The corresponding results reveal contrasting thermal regimes at depths (Buenavista: 101–122 °C, El Sargento: 212–220 °C), likely associated with differences in geothermal gradient and fluid circulation depth. Our gas samples have among the lowest He isotopic ratios (0.07–0.95 Ra) in the Baja California peninsula, indicating that the origin of helium is mainly crustal. Shear wave tomography demonstrates that the study area is associated with two low velocity regions, one in the crust and the other one in the upper mantle. Our results favor the hypothesis that the heating of fluids is produced by lower-crustal flow driven by strong topographic gradients along the rifted margin. This study provides new insights into the origin of the thermal anomalies in the LCB and the adjacent GC rift system.