Pressure to decrease reliance on surface water storage has led to increased interest in aquifer storage and recovery (ASR) systems. Recovery efficiency, which is the ratio of the volume of recovered water that meets a predefined standard to total volume of injected fluid, is a common criterion of ASR viability. Recovery efficiency can be degraded by a number of physical and geochemical processes, including rate-limited mass transfer (RLMT), which describes the exchange of solutes between mobile and immobile pore fluids. RLMT may control transport behavior that cannot be explained by advection and dispersion. We present data from a pilot-scale ASR study in Charleston, South Carolina, and develop a three-dimensional finite-difference model to evaluate the impact of RLMT processes on ASR efficiency. The modeling shows that RLMT can explain a rebound in salinity during fresh water storage in a brackish aquifer. Multicycle model results show low efficiencies over one to three ASR cycles due to RLMT degrading water quality during storage; efficiencies can evolve and improve markedly, however, over multiple cycles, even exceeding efficiencies generated by advection-dispersion only models. For an idealized ASR model where RLMT is active, our simulations show a discrete range of diffusive length scales over which the viability of ASR schemes in brackish aquifers would be hindered.