Ocean acidification is changing surface water chemistry, but natural variability due to nearshore processes can mask its effects on ecosystem responses. We present an approach of quantitatively resolving net ecosystem metabolism from an array of long-term time series stations, offering perhaps the longest record of such processes over a reef to date. We used 8 and 6 yr of in situ, high-quality frequency observations to characterize the changes in dissolved inorganic carbon and oxygen in La Parguera, Puerto Rico and Cheeca Rocks, Florida, respectively. Net respiration and net dissolution are the dominant metabolic processes at both systems, with a narrow window of ~ 4 months under net calcification. The annual mean net ecosystem calcification (NEC) rates for La Parguera (−0.68 ± 0.91 kg CaCO₃ m⁻² yr⁻¹) and Cheeca Rocks (−0.48 ± 0.89 kg CaCO₃ m⁻² yr⁻¹) were on the lower end of typical NEC ranges determined for other reef areas using chemistry- and census-based approaches. At Cheeca Rocks, 53% of the variance in NEC can be explained by net ecosystem production (NEP) and 30% by aragonite saturation state (Ω_arag). At La Parguera, NEC is primarily driven by changes in NEP. The linear relationship between NEC and NEP showed a significant slope (± standard error) of 1.00 ± 0.005 and 0.88 ± 0.04 for La Parguera and Cheeca Rocks, respectively. These results suggest that NEP appears to play a prominent role on NEC, and Ω_arag probably is not the most informative measure to monitor when attempting to resolve the long-term impacts of ocean acidification.