A notable drawback in mixed-size sediment morphodynamic modeling is the fact that the most commonly used mathematical model in this field (i.e., the active layer model Hirano, 1971) can be ill-posed under certain circumstances. Under these conditions the model loses its predictive capabilities, as negligible perturbations in the initial or boundary conditions produce significant differences in the solution. In this paper we propose a preconditioning method that regularizes the model to recover well-posedness by altering the time scale of the sediment mixing processes. We compare results of the regularized model to data from four new laboratory experiments conducted under conditions in which the active layer model is ill-posed. The regularized active layer model captures the change of bed elevation and surface texture averaged over the passage of several bedforms. Neither the active layer model nor the regularized one account for small scale changes due to individual bedforms.