Estimating the current sources and sinks of carbon and projecting future levels of CO2 and climate require biospheric carbon models that cover the landscape. Such models inevitably suffer from deficiencies and uncertainties. This paper addresses how to quantify errors in modeled carbon fluxes and then trace them to specific input variables. To date, few studies have examined uncertainties in biospheric models in a quantitative fashion that are relevant to landscape-scale simulations. In this paper, we introduce a general framework to quantify errors in biospheric carbon models that “unmix” the contributions to the total uncertainty in simulated carbon fluxes and attribute the error to different variables. To illustrate this framework we apply and use a simple biospheric model, the Vegetation Photosynthesis and Respiration Model (VPRM), in boreal forests of central Canada, using eddy covariance flux measurement data from two main sites of the Canadian Carbon Program (CCP). We explicitly distinguish between systematic errors (“biases”) and random errors and focus on the impact of errors present in biospheric parameters as well as driver data sets (satellite indices, temperature, solar radiation, and land cover). Biases in downward shortwave radiation accumulated to the most significant amount out of the driver data sets and accounted for a significant percentage of the annually summed carbon uptake. However, the largest cumulative errors were shown to stem from biospheric parameters controlling the light-use efficiency and respiration-temperature relationships. This work represents a step toward a carbon model-data fusion system because in such systems the outcome is determined as much by uncertainties as by the measurements themselves.