We employ a coarse-graining approach to analyze non-linear cascades in Boussinesq flows using high-resolution simulation data. We derive budgets which resolve the evolution of energy and potential enstrophy simultaneously in space and in scale. We then use numerical simulations of Boussinesq flows, with forcing in the large scales, and fixed rotation and stable stratification along the vertical axis, to study the inter-scale flux of energy and potential enstrophy in three different regimes of stratification and rotation: i) strong rotation and moderate stratification, ii) moderate rotation and strong stratification, and iii) equally strong stratification and rotation. In all three cases, we observe constant fluxes of both global invariants, the mean energy and mean potential enstrophy, from large to small scales. The existence of constant potential enstrophy flux ranges provides the first direct empirical evidence in support of the notion of a cascade of potential enstrophy. The persistent forward cascade of the two invariants reflects a marked departure of these flows from two-dimensional turbulence.