We consider the time dependent Darcy problem in a three-dimensional axisymmetric domain and, by writing the Fourier expansion of its solution with respect to the angular variable, we observe that each Fourier coefficient satisfies a system of equations on the meridian domain. We propose a discretization of these equations in the case of general solution. This discretization relies on a backward Euler’s scheme for the time variable and finite elements for the space variables. We prove a posteriori error estimates that allow for an efficient adaptivity strategy both for the time steps and the meshes. Computations for an example with a known solution are presented which support the a posteriori error estimate.