The supply of water to the Nueces River Delta near Corpus Christi, Texas is limited by dams and channelization of the river which restrict freshwater inflow. The upper end (high marsh) of the delta frequently dries up during the summer. The marsh consists of slightly elevated islands containing emergent halophytes, and shallow ponds interconnected by narrow channels. Carbon dioxide exchange in the marsh was measured by relaxed eddy accumulation (REA) during two periods, one in 1997 that included two floods from the river followed by an extended period of drying and disappearance of standing water, and the other in 1998 that was in the midst of a drought with no standing water present. The marsh was a net CO2 sink during periods of high water availability and low sediment salinity, and a net source when water availability was low and salinity was high. During the 1997 period, net ecosystem exchange (NEE) and gross ecosystem production (GEP) ranged from −7.3 g CO2 m−2 per day (net gain of CO2) and 12.3 g CO2 m−2 per day, respectively, after flooding to +8.7 g CO2 m−2 per day (net loss of CO2) and 0.4 g CO2 m−2 per day, respectively, when sediments were dry. NEE and GEP averaged 0.5 and 7.7 g CO2 m−2 per day, respectively, during this period. Standing water, and water in pores restricted gas exchange between sediment and the atmosphere so that ecosystem respiration (R) increased as the marsh dried, with R ranging from 1.2 to 15.6 g CO2 m−2per day and averaging 8.2 g CO2 m−2 per day. During the 1998 drought, NEE, GEP, and R averaged 5.8, 3.3, and 9.1 g CO2 m−2 per day, respectively. A 27 mm rain during this period produced a 14-fold increase in GEP and a 75% reduction in R that lasted for 2 days. In 1997, NEE and its components were all significantly correlated at the 0.05 level with water availability as estimated by the cumulative difference between rainfall and evaporation, while in 1998, only NEE and GEP were significantly correlated with water availability. Results of this study indicate that the marsh NEE behaved more like that of a dryland ecosystem than a wetland because of limited freshwater inflow.