Part of the inaccuracies when estimating bed load transport in gravel-bed rivers is because we are not considering the wide distributions of shear stress in these systems. We modified a subsurface-based bed load transport equation to include these distributions. By doing so, our approach accurately predicts bed load transport rates when the pavement layer is still present, while the original one predicts zero transport. For high flows, our method had similar performance to the original equation.