Coastal settings variations are linked to composition, structural and functional differences among mangrove ecotypes. Basin mangroves undergo larger flooding and salinity fluctuations, yet remain understudied, compared to other ecotypes. We evaluated the effect of flooding and air temperature (Ta) on the surface energy balance and eddy covariance‐derived net CO2 ecosystem exchange (NEE) of a basin mangrove with sporadic freshwater flooding. During the study period (Jun 2017–Nov 2018) the site was more frequently not flooded. Under these conditions, in combination with high Ta (>27°C), daytime CO2 uptake was significantly lower, while evapotranspiration and sensible heat flux were higher than when flooded. CO2 uptake increased with Ta and vapor pressure deficit, but after exceeding a threshold (29°C and 1.4 kPa), uptake declined. Flooding extended this Ta threshold by 3°C and increased the radiation saturation point of NEE. The ecosystem is a net sink of CO2 annually (709±09 g C m−2 yr−1), however, it turned a net source of CO2 for three months of prolonged rainfall deficit. Most of the precipitation input is returned to the atmosphere (evaporative index: 0.94) and on average, for each gram of atmospheric carbon assimilated into the ecosystem, 2.21±0.50 kg of water was returned to the atmosphere. This ecosystem‐level water‐use efficiency decreased with flooding, but the correlation was not strong. Future temperature increases and lower precipitation (local and regional), combined with lower water table (and/or stronger saline intrusion), imply important losses of primary productivity and stored soil carbon in basin mangroves of northeast Yucatan Peninsula.