Data were obtained to assess net ecosystem exchange of CH4 and CO2 in tidal freshwater and brackish marshes. These data represent net ecosystem exchange of CH4 and CO2 collected using eddy covariance over various time frames. Data were collected from a brackish marsh at Pointe-aux-Chenes State Wildlife Management Area and a tidally influenced freshwater marsh at Salvador State Wildlife Management Area. Both sites were located within the coastal zone of Louisiana, USA.