In the present study we have modeled the groundwater inputs to the only permanent pond of Doñana Biological Reserve (Andalusia, Southern Spain) by means of the application of a thermal modelling methodology. During the study period (February-May 2017) a chain of thermistors obtained hourly temperature data from the water column and the sediment below. In addition, water level in the pond and in the aquifer near the shores was also monitored at similar time rates. Results showed that a net groundwater discharge is produced heterogeneously through the pond’s bed. The comparison of these outcomes with previous studies made in the pond (hydrological water balances, hydrogeological methods applying Darcy’s equation) is coherent and strengthens the existing hydrological knowledge of this water body. Finally, it has been detected that the pond is in a sharp relation with the alterations of the sand aquifer, even if such alterations are produced away from the pond an at high depths. The effects of groundwater extractions for urban supply of a nearby coastal resort are immediately affecting the evolution of the water level, although this affection is not necessarily traduced onto water level depletion. Most probably, the effect is produced by an elastic rebound of the groundwater in the aquifer.