The presence of solute concentration fluctuations at spatial scales much below the working scale is a major challenge for modeling reactive transport in porous media. Overlooking small-scale fluctuations, which is the usual procedure, often results in strong disagreements between field observations and model predictions, including, but not limited to, the overestimation of effective reaction rates. Existing innovative approaches that account for local reactant segregation do not provide a general mathematical formulation for the generation, transport and decay of these fluctuations and their impact on chemical reactions. We propose a Lagrangian formulation based on the random motion of fluid particles whose departure from the local mean concentration is relaxed through multi-rate interaction by exchange with the mean (MRIEM). We derive and analyze the macroscopic description of the local concentration covariance that emerges from the model and show that mixing-limited processes can be properly simulated. The action of hydrodynamic dispersion on coarse-scale concentration gradients is responsible for the production of local concentration covariance, whereas covariance destruction stems from the local mixing process represented by the MRIEM formulation. The temporal evolution of integrated mixing metrics in two simple scenarios shows the trends that characterize fully-resolved physical systems, such as a late-time power-law decay of the relative importance of incomplete mixing with respect to the total mixing. Experimental observations of mixing-limited reactive transport are successfully reproduced by the model.