Methane and nitrous oxide are potent greenhouse gases whose atmospheric abundances have increased significantly in the past 200 years, together accounting for approximately half of the radiative forcing associated with increasing concentrations of carbon dioxide. In order to understand the factors causing increase of these gases globally, we need to determine their emission rates at regional to continental scales. We directly link atmospheric observations with surface emissions using a Lagrangian Particle Dispersion Model, and then determine emission rates by optimizing prior emissions estimates. We use measurements from NOAA's tall tower and aircraft program in 2004, The Stochastic Time-Inverted Lagrangian Transport model (STILT) driven by meteorological fields from a customized version of the Weather Research and Forecasting (WRF) model, and EDGAR32FT2000 and Global Emissions Inventory Activity (GEIA) as prior emission estimates. In the US and Canada, methane emission rates are found to be consistent with observations, while nitrous oxide emissions are significantly low, by a factor 2.5–3 in the peak emissions time period found to be February through May.