The metabolism of Cayo Enrique Reef, Puerto Rico, was studied using in situ methods during March 2009. Benthic O2 fluxes were used to calculate net community production using both the boundary layer gradient and enclosure techniques. The boundary layer O2 gradient and the drag coefficients were used to calculate productivity ranging from -12.3 to 13.7 mmol O2 m-2 h-1. Productivity measurements from the enclosure method ranged from -11.0 to 12.9 mmol O2 m-2 h-1. During the study, the mean hourly difference between the methods was 0.65 mmol O2 m-2 h-1 (r2 = 0.92), resulting in well-reconciled estimates of net community production between the boundary layer (-33.1 mmol m-2 d-1) and enclosure (-46.3 mmol m-2 d-1) techniques. The results of these independent approaches corroborate quantified rates of metabolism at Cayo Enrique Reef. Close agreement between methods demonstrates that boundary layer measurements can provide near real-time assessments of coral reef health.