Methods description:
Total alkalinity (TA) and dissolved inorganic carbon (DIC) spatial surveys were conducted across the entire Kāneʻohe Bay barrier reef flat including samples offshore from the reef flat boundary on 31 October 2015, 31 June 2016, 12 November 2016, and 26 February 2017. At each station, surface temperature and salinity were measured with handheld YSI multiprobes and seawater samples were collected by hand at the surface following standard protocols for analysis of TA and DIC.

Analytical Methods:
Surface seawater samples were collected by hand at ~0.25 m depth using 250 ml Pyrex glass bottles and immediately fixed with 100 µL HgCl2 as per standard protocols (Dickson et al. 2007). Handheld YSI multiprobes (October 2015: YSI 6600 V2; June 2016, November 2016: YSI Professional Plus; February 2017: YSI 556) were calibrated and used to measure temperature and salinity at the time of sampling. All seawater samples were transported to the Scripps Coastal and Open Ocean Biogeochemistry lab and analyzed for TA via an open-cell potentiometric acid titration system developed at Scripps Institution of Oceanography (SIO) by A. Dickson (Dickson et al. 2007) and DIC via an automated infra-red inorganic carbon analyzer (AIRICA, Marianda Inc).

Quality Control:
Standard protocols were followed for sampling and analysis of seawater TA and DIC. YSI multiprobes were calibrated prior to each sampling with an accuracy of ±0.2°C for temperature and ±0.3 g kg-1 for salinity. The mean accuracy (TA±1.3 µmol kg-1, DIC ±1.6 µmol kg-1) and precision (TA±1.3 µmol kg-1, DIC ±1.4 µmol kg-1) of TA and DIC measurements were evaluated using certified reference materials (CRM) provided by the laboratory of A. Dickson at SIO and analyzed every 5 samples for DIC and ~10-15 samples for TA.