Micrometeorological methods provide a selection of techniques for quantifying the fluxes of energy and gases from the soil surface to the atmosphere. The advantages of these methods are the non-disturbance of the surface and the ability to continually monitor fluxes over a range of surfaces and of different gases.  Quantification of carbon dioxide, methane, and nitrous oxide fluxes from agricultural systems is critical to understanding the effects of different agronomic management practices on these emissions.  Observations have been collected on carbon dioxide fluxes coupled with water vapor fluxes over corn and soybean canopies throughout the complete year.  The coupling of carbon dioxide and water vapor fluxes over crop canopies allows for a more complete understanding of the processes controlling greenhouse gas fluxes relative to biophysical crop canopy processes.  Carbon dioxide and water vapor fluxes are measured with open path fast-response systems that permit analysis of the time series responses to surface changes. Methane and nitrous oxide fluxes can be measured with samplers that can be easily linked with sonic anemometers or wind profile anemometers to quantify the fluxes.  Micrometeorological methods permit analysis of both the short time scale (minutes) up to an integration over daily or longer time scales.  Observations collected over different tillage or fertilizer management systems have provided new insights into the dynamics that control greenhouse gas fluxes.