• salt marsh;
  • wetland;
  • flood;
  • evapotranspiration;
  • energy balance;
  • photosynthesis

[1] The degree to which short-duration, transient floods modify wetland-atmosphere exchange of energy, water vapor, and carbon dioxide (CO2) is poorly documented despite the significance of flooding in many wetlands. This study explored the effects of transient floods on salt marsh–atmosphere linkages. Eddy flux, micrometeorological, and other field data collected during two tidal phases (daytime versus nighttime high tides) quantified the salt marsh radiation budget, surface energy balance, and CO2 flux. Analysis contrasted flooded and nonflooded and day and night effects. The salt marsh surface energy balance was similar to that of a heating-dominated sparse crop during nonflooded periods but similar to that of an evaporative cooling-dominated, well-watered grassy lawn during flooding. Observed increases in latent heat flux and decreases in net ecosystem exchange during flooding were proportional to flood depth and duration, with complete CO2 flux suppression occurring above some flood height less than the canopy height. Flood-induced changes in the salt marsh energy balance were dominated by changes in sensible heat flux, soil heat flux, and surface water heat storage. Parameters suitable for predicting the salt marsh surface energy balance were obtained by calibrating common models (e.g., Penman-Monteith, Priestley-Taylor, and pan coefficient). Biophysical controls on salt marsh–atmosphere exchange were identified following calibration of models describing the coupling of canopy photosynthesis and stomatal conductance in the salt marsh. The effects of flooding on salt marsh–atmosphere exchange are temporary but strongly affect the marsh water, carbon, and energy balance despite their short duration.