Accurate predictions of how coral reefs may respond to global climate change hinge on understanding the natural variability to which these ecosystems are exposed and to which they contribute. We present high-resolution estimates of net community calcification (NCC) and net community production (NCP) from Palmyra Atoll, an uninhabited, near-pristine coral reef ecosystem in the central Pacific. In August–October 2012, we employed a combination of Lagrangian and Eulerian frameworks to establish high spatial (~2.5 km2) and temporal (hourly) resolution coral community metabolic estimates. Lagrangian drifts, all conducted during daylight hours, resulted in NCC estimates of −51 to 116 mmol C m−2 h−1, although most NCC estimates were in the range of 0–40 mmol C m−2 h−1. Lagrangian drift NCP estimates ranged from −7 to 67 mmol C m−2 h−1. In the Eulerian setup, we present carbonate system parameters (dissolved inorganic carbon, total alkalinity, pH, and pCO2) at sub-hourly resolution through several day–night cycles and provide hourly NCC and NCP rate estimates. We compared diel cycles of all four carbonate system parameters to the offshore surface water (0–50 m depth) and show large departures from offshore surface water chemistry. Hourly Eulerian estimates of NCC aggregated over the entire study ranged from 14 to 53 mmol C m−2 h−1, showed substantial variability during daylight hours, and exhibited a diel cycle with elevated NCC in the afternoons and depressed, but positive, NCC at night. The Eulerian NCP range was very high (−55 to 177 mmol C m−2 h−1) and exhibited strong variability during daylight hours. Principal components analysis revealed that NCC and NCP were most closely aligned with diel cycle forcing, whereas the NCC/NCP ratio was most closely aligned with reef community composition. Our analysis demonstrates that ecological community composition is the primary determinant of coral reef biogeochemistry on a near-pristine reef and that reef biogeochemistry is likely to be responsive to human behaviors that alter community composition.