The future carbon (C) balance of high latitude ecosystems is dependent on the sensitivity of biological processes (photosynthesis and respiration) to the physical changes occurring with permafrost thaw. But predicting C exchange in these ecosystems is difficult because the thawing of permafrost is not a uniform and homogeneous process. We measured net ecosystem exchange (NEE) of C using eddy covariance (EC), in a tundra landscape visibly undergoing thaw, during two 6-month campaigns in 2008 and 2009. We developed a spatially explicit quantitative metric of permafrost thaw based on variations in microtopography and incorporated it into an EC carbon flux estimate using a generalized additive model (GAM). This model allowed us to make predictions about C exchange for the landscape as a whole, and for specific landscape patches throughout the continuum of permafrost thaw and ground subsidence. Our objective was to estimate the C balance of a heterogeneous landscape and more accurately determine the collective effect of permafrost thaw on ecosystem C balance. During June through November of 2008, the GAM predicted the landscape on average took up 337.1 gCm-2 and released 289.5 gCm-2, resulting in a net C gain of 47.5 gCm-2. During April through October of 2009, the landscape on average took up 498.7 gCm-2 and released 410.3 gCm-2, resulting in a net C gain of 87.8 gCm-2. On average between the years, areas with the highest permafrost thaw took up 17.7% more and respired 3.3% more C than the average landscape. Areas with the least thaw took up 15% less and respired 5.1% less than the landscape on average. By incorporating spatial variation into the EC C estimate, we were able to determine how thaw affect C flux. Overall, permafrost thaw increases the amplitude of the C cycle by stimulating both C release and sequestration.