We describe a system for making real-time measurements and analyses of metabolic rates of communities in flowing water. Oxygen sensors, a current meter, a light meter, and a tide gauge were connected to a microcomputer that monitored the changes in oxygen concentration of a reef flat community in situ and in a continuous flow microcosm. This system enabled the observation of the response of community metabolism to short-term environmental changes, such as clouds passing over the sun, and provided estimates of long-term rates. Along the reef transect, net daily production was 30.3 g 0, (11.4 g C) m-2, total night respiration was -13.3 g 0, (-5.0 g C) m-2, and daily excess production was 17.0 g 0, (6.4 g C) m-2. In the microcosm net daily production was 4.1 g 0, (1.5 g C) m-2, total night respiration was -2.3 g O2 (-0.9 g C) m-2, and daily excess production was 1.8 g 0, (0.7 g C) m-2. Primary production of both reef and microcosm saturated at relatively high irradiance (values of Zk > 600 PEinst m-2 s-l; of Zg5% > 1,100 PEinst m-2 s-l).