Primary production, respiration, and net ecosystem metabolism (NEM) are useful indicators of ecosystem level trophic conditions within estuaries. In this study, dissolved oxygen data collected every half hour between January 1996 to December 1998 by the National Estuarine Research Reserve System Wide Monitoring Program were used to calculate primary production, respiration, and net ecosystem metabolism. Data from two sites at each of 14 Reserves were analyzed. On average, three quarters of the data available could be used to calculate metabolic rates. Data from two of the Reserves were used to evaluate the assumption of homogeneity of water masses moving past the oxygen sensor. Temperature was the single most important factor controlling metabolic rates at individual sites, although salinity was also important at about half the sites. On an annual basis, respiration exceeded gross primary production demonstrating that all but 4 of the 28 sites were heterotrophic.