Net ecosystem exchange (NEE) is an essential climate indicator of the direction and magnitude of carbon dioxide (CO2) transfer between land surfaces and the atmosphere. Improved estimates of NEE can serve to better constrain spatiotemporal characteristics of terrestrial carbon fluxes, improve verification of land models, and advance monitoring of Earth's terrestrial ecosystems. Spatiotemporal NEE information developed by combining ground-based flux tower observations and spatiotemporal remote sensing datasets are of potential value in benchmarking land models. We apply a machine learning approach (Random Forest (RF)) to develop spatiotemporally varying NEE estimates using observations from a flux tower and several variables that can potentially be retrieved from satellite data and are related to ecosystem dynamics. Specific variables in model development include a mixture of remotely sensed (fraction of photosynthetically active radiation (fPAR), Leaf Area Index (LAI)) and ground-based data (soil moisture, downward solar radiation, precipitation and mean air temperature) in a complex landscape of the Reynolds Creek Experimental Watershed (RCEW) in southwest Idaho, USA. Predicted results show good agreement with the observed data for the NEE (r2 = 0.87). We then validate the temporal pattern of the NEE generated by the RF model for two independent years at the two sites not used in the development of the model. The model development process revealed that the most important predictors include LAI, downward solar radiation, and soil moisture. This work provides a demonstration of the potential power of machine learning methods for combining a variety of observational datasets to create spatiotemporally extensive datasets for land model verification and benchmarking.