Electromagnetic (EM) heating is an emerging method for storing renewable energy, such as photovoltaic solar and wind electric power, into aquifers. We investigate how the captured energy increases the temperature of a prototypical deep aquifer for a six-month period and then to which extent the stored energy can be recovered during the consecutive six months. Water injected at a constant flow rate is simultaneously heated using a high-frequency electromagnetic microwave emitter operating at the water natural resonance frequency of 2.45 GHz. The coupled reservoir flow and EM heating are described using Darcy’s and the energy balance equations. The latter includes a source term accounting for the EM wave propagation and absorption, modeled separately using Maxwell’s equations. The equations are solved numerically by the Galerkin least-squares finite element method. The approach was validated using EM-heating input data obtained from controlled laboratory experiments and then was applied to the aquifer. We found that after six years of alternate storage and recovery, up to 77% of the injected energy is recovered when considering realistic heat losses estimated from field data. Even when heat losses are increased by a factor of two, up to 69% of the injected energy is recovered in this case. This shows that down-hole EM heating is a highly effective method for storing renewable energies, capable of helping to solve their inherent intermittency.