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Growing season soil CO2 efflux is known to vary laterally by as much as seven fold within small subalpine watersheds (<5 km2), and such degree of variability has been strongly related to the landscape-imposed redistribution of soil water. Current empirical or process models offer low potential to simulate this variability or to simulate watershed-scale dynamics of soil CO2 efflux. We modified an existing process soil CO2 production and efflux model to include spatially variable soil moisture, and applied it to a well-studied and moderately complex watershed of the northern Rocky Mountains. We started at the point scale and progressively modeled processes up to the watershed scale. We corroborated model performance using an independent data set of soil CO2 efflux measurements from 53 sites distributed across the 393 ha watershed. Our approach simulated the seasonality of soil CO2 efflux at riparian sites; (2) reproduced short-term (diel) dynamics of soil CO2 concentration ([CO2]) at riparian sites, particularly observed hysteresis patterns in the soil [CO2]–soil temperature relationship; and (3) simulated growing season estimates of soil CO2 efflux at dry sites across the landscape (98% of area). Model limitations included poor simulation of growing season (cumulative) soil CO2 efflux at sites with a large drainage area, likely as a result of poorly modeled soil water content and challenges in parametrization of root and microbial activities. Our study provides important insight into coupling hydrological and biogeochemical models at landscape scales, and highlights the role of landscape structure and heterogeneity when modeling spatial variability of biogeochemical processes.