Published frequency-domain solutions of periodic flow in aquifers apply strictly to mathematically linear systems that arise when aquifer diffusivity is assumed constant in space and time. This assumption can be invalid in phreatic aquifers that experience spatiotemporal variation in the free surface position and consequent variation in saturated thickness. A weakly nonlinear approach to formulating and solving periodic flow problems in the frequency domain can be applied in situations where conventional linearized approximations break down. The weakly nonlinear equations provide robust approximations of the true nonlinear response and require much less computational effort and time to solve than the full nonlinear problem. Nondimensional rules of thumb are presented for choosing between linear, weakly nonlinear and nonlinear solution strategies.