Critical zone evolution, structure, and function are driven by energy and mass fluxes into and through the terrestrial subsurface. We have developed an approach to quantifying the effective energy and mass transfer (EEMT, MJ m−2 yr−1) to the subsurface that accounts for local variations in topography, water and energy balances, and primary production. Our objectives were to quantify how (i) local topography controls coupled energy and water transfer to the subsurface, and (ii) vegetation effects on local-scale evapotranspiration and primary production controls of energy and mass transfer to the critical zone, both at the pedon- to hillslope-scale resolution, in the context of quantifying controls on EEMT. The model was tested across a semiarid environmental gradient in southern Arizona, spanning desert scrub to mixed conifer ecosystems. Data indicated clear variations in EEMT by topography, via both aspect and local water redistribution, and with current vegetative cover. Key findings include: (i) greater values of EEMT on north-facing slopes in a given elevation zone, with a north-facing aspect equivalent to an ∼300-m elevation gain; (ii) a power law relationship between aboveground biomass and EEMT, with disturbance in the form of stand-replacing wildfire substantially reducing estimates of EEMT; and (iii) improved correlation of EEMT to pedon-scale variations in critical zone structure with EEMT values that include topography. Incorporating greater levels of environmental variation and complexity presents an improved approach to estimating the transfer of energy and mass to the subsurface, which is important to our understanding of critical zone structure and function.