In this work, transient source terms in advection-diffusion problems are recovered. The solution technique proposed relies on the implicit finite difference method coupled with the method of fundamental solutions, a technique for solving partial differential equations when their fundamental solution is known. The Truncated Singular Value Decomposition was used to overcome the ill-conditioned resulting linear system. The advection-diffusion inverse problem was solved using a Eulerian–Lagrangian method. Several numerical examples were considered for testing purposes by using simulated measurements perturbed with a Gaussian random noise for different Reynolds numbers. Results show that the proposed method provides stable and accurate estimates for the source term.