We have determined the present thermal state of the impact crater. In a preliminary step we established the first 3-D sub-surface structural model of Chicxulub impact crater. The complete gravity data set of northern Yucatan was inverted to obtain the topography of the central basin including the structural high. 2-D Euler deconvolution helped in locating the sources of the magnetic anomalies (i.e., melt/breccia sequence). The deeper magnetic sources correlate with the central uplift as obtained from the gravity inversion. Magnetic sources above the central uplift may correspond to melted rock. The information from boreholes drilled by the Universidad Nacional Autónoma de México (UNAM) was used to complement the information from the gravity and magnetic study. This 3-D model was subsequently used to establish the thermal state of the impact basin and its relation to the ground water flow. We determined the heat flow from a geothermal study based in the boreholes drilled by UNAM. The mean temperature gradient in the study area is 0,03 °C/m. The thermal conductivity varies from 2,11 to 2,67 W/m°C for the different rock types present. We obtain a mean heat flow of 64 ± 8 mW/m². Based in all this information we modeled the conduction-convection heat and mass transfer in the 3-D established model. We used a dimensionless formulation assuming an axisymmetric geometry for the crater. An appropriate change of variable reduced the 3-D axisymmetric problem to a 2-D Cartesian one. With this formulation the heat and Darcy coupled equations become similar and can be solved with the same kind of numerical algorithm. The results confirm that the flow of water is controlled by the crater structure, and modifies the thermal state (as inferred, for example, in the temperature profiles). We observe smaller heat flow values at the rim of the crater than at its center (20 and 60 mW/m² respectively). The circulation of underground water through the fractured limestone is the cause of a generally low heat flow in the rim of this structure.