•NEE during neap tides was ~ 60% greater than during spring high tides•The effect of tidal flooding on NEE varied with the degree of plant inundation•The highest CO2 flux reductions were observed in early and peak growing seasons•Daytime CO2 flux was reduced 20-60% in the peak growing season due to tidal flooding Salt marshes are highly productive ecosystems and yet we have only a preliminary understanding of how net ecosystem exchange varies on daily and seasonal time scales. We used the eddy-covariance method to examine the behaviour of the net ecosystem exchange as influenced by tidal flooding in daytime conditions in a coastal salt marsh dominated by Spartina alterniflora in Georgia, USA. Two different analyses both found that the net ecosystem exchange was ~ 60% greater during neap high tides than during spring high tides; the largest differences occurred early in the growing season. The effect of tidal flooding varied continuously with the degree to which plants were inundated versus emergent. The total monthly reduction (less negative) in daytime net ecosystem exchange due to flooding was 7-38% and 1-64% in 2014 and 2015 respectively. The highest CO2 flux reductions were observed early and during the peak growing season (February, March, April and May) and the lowest during the summer season in both years. Our findings suggest that daytime CO2 flux was reduced (less negative) 20-60% during the peak growing season due to tidal flooding. A better understanding of the impact of seasonal tidal flooding on net ecosystem exchange may allow more sophisticated predictions of how sea level rise will affect marsh function and survival over the coming century.