A hydrogeological conceptual model has been developed that describes the geothermal system located at the Maneadero region in Ensenada, Baja California, Mexico. In addition, a two-dimensional steady state simulation of water flow and heat transfer of a model profile using COMSOL Multiphysics software is also presented. The proposed hydrogeological conceptual model considers that the old local anoxic subsurface seawater feeds the system, and a remnant magmatic intrusion in the surface from past volcanism at 2 km of depth works as heat source. The intersection between the south Agua Blanca Fault and the L3 alignment promote the fluids ascent to the submarine hydrothermal vent. The results of the simulation show a reservoir temperature of 164 °C and an affluent temperature of 105 °C, varying between 1 °C and 3 °C, respectively, with previous studies. Moreover, a geothermal potential of 0.48 MW was estimated for the simulated profile. The current policy of exploitation of geothermal resources in Mexico makes the development of these models particularly relevant, serving as a tool for their evaluation and management.