Micrometeorological flux towers provide spatially integrated estimates of net ecosystem production (NEP) of carbon over areas ranging from several hectares to several square kilometers, but they do so at the expense of spatially explicit information within the footprint of the tower. This finer-scale information is crucial for understanding how physical and biological factors interact and give rise to tower-measured fluxes in complex landscapes. We present a simple approach for quantifying and evaluating the spatial heterogeneity of cumulative growing season NEP for complex landscapes. Our method is based on spatially distributed information about physical and biological landscape variables and knowledge of functional relationships between constituent fluxes and these variables. We present a case study from a complex landscape in the Rocky Mountains of Montana (US) to demonstrate that the spatial distribution of cumulative growing season NEP is rather large and bears the imprint of the topographic and vegetation variables that characterize this complex landscape. Net carbon sources and net carbon sinks were distributed across the landscape in manner predictable by the intersection of these landscape variables. We simulated year-to-year climate variability and found that some portions of the landscape were consistently either carbon sinks or carbon sources, but other portions transitioned between sink and source. Our findings reveal that this emergent behavior is a unique characteristic of complex landscapes derived from the interaction of topography and vegetation. These findings offer new insight for interpreting spatially integrated carbon fluxes measured over complex landscapes.