Optical in situ chemical sensors enable sampling intervals and durations that rival acoustic techniques used for measuring currents. Coupling these high-frequency biogeochemical and physical measurements in estuaries to address ecosystem-scale questions, however, is still comparatively novel. This study investigated how tides affect ecosystem metabolism in a mesotidal estuary in central California (Elkhorn Slough). Dissolved oxygen measurements were used to estimate the terms in a control volume budget for a tidal creek/marsh complex at tidal timescales over several weeks. Respiration rates were 1.6 to 7.3 g O2 m−2 day−1; net community production approached 20 g O2 m−2 day−1. We found that aquatic NCP integrated throughout the creek complex varied significantly over the spring-neap cycle. The intertidal contribution to aquatic metabolism was net heterotrophic during spring tides and generally in balance during neap tides because spring-tide marsh inundation was limited to nighttime, and therefore the marsh could not contribute any primary production to the water column. At the estuary scale, the fortnightly export of oxygen from the main channel to the intertidal was largely balanced by an advective flux up-estuary.