Net ecosystem calcification (NEC) and net photosynthesis (NP) were measured on the barrier coral reef of Kaneohe Bay, Oahu, Hawaii. Autosamplers were deployed on the barrier reef to collect samples for total alkalinity (TA) and dissolved inorganic carbon (DIC) analyses every 2 hours for six 48 hour deployments from 2008–2010. In addition, a Coral Reef Instrumented Monitoring and CO₂-Platform (CRIMP-CO₂) mooring was deployed in the southern Kaneohe Bay lagoon from 2005–2007, then on the barrier reef from 2008–2010. NEC on the barrier reef increased throughout the day and decreased at night. The barrier reef was generally net photosynthetic during the day and net respiring at night. NP controlled the diet cycles of seawater pCO₂ and Ω_arag in Kaneohe Bay. The amplitudes of the diel cycles of pCO₂ and Ω _arag were 6–7 times greater on the shallow barrier reef than in deeper lagoon waters. On a net daily basis the barrier reef was net calcifying for all deployments (174 to 331 mmol CaCO₃ m⁻² d⁻¹) and daily NEC was negatively correlated with pCO ₂ (R² = 0.76). Net calcification in Kaneohe Bay elevated surface water pCO₂ relative to open ocean waters and other coral reef ecosystems. Daily NEC of the barrier reef is similar to or higher than NEC measured on other coral reef ecosystems though Ω_arag is low (mean Ω _arag = 2.85 ± 0.37) compared to other coral reefs. These results suggest that while NEC and pCO₂ are correlated within a single coral reef ecosystem, this correlation varies between different coral reefs. Surface water pCO₂ was higher during the summer than winter in Kaneohe Bay because temperature was also higher in summer. Temperature and pCO_2sw have opposing effects on Ω_arag which resulted in a lack of seasonality in Ω_arag. Similarly, average daily NEC was not significantly different between summer and winter. Coral reefs are dynamic ecosystems that experience large natural swings in pCO₂ over short periods of time. Measurements must be made within these systems, not just in the open ocean waters surrounding them, in order to evaluate the effects of ocean acidification on coral reef NEC.