Eddy covariance is the most direct method for measuring surface atmosphere exchange of heat and mass. However, poor energy balance closure and other anomalies suggest there are still theoretical and experimental issues that need attention. Several authors have suggested that lack of closure is caused by low frequency transport process caused by spatial heterogeneity in the landscape. A fraction of these fluxes are missed (i.e., inadvertently filtered) when the standard 30-min integration period is used. Also, many researchers collect 10 Hz time-series data, but this sampling rate may be too slow above in soils, crops, and grasslands where data are collected only 2 to 3 m above the surface. A study of these issues was conducted using data from a network of eddy covariance towers deployed in central and eastern Kansas, USA. Results will show how both low and high frequency transport process may be affecting measurements of heat, CO2, and water vapor when using eddy covariance.