Netarts Bay is a shallow, temperate, tidal lagoon located on the northern coast of Oregon and site of the Whiskey Creek Shellfish Hatchery (WCSH). Data collected with an automated flow-through system installed at WCSH capable of high-resolution (1 Hz) pCO2 and hourly TCO2 measurements, with measurement uncertainties of <2.0% and 0.5%, respectively, is analyzed over the 2014-2019 interval. These measurements provide total constraint on the carbonate system, allowing calculation of carbonate variables such as pHt, alkalinity, and carbonate mineral saturation states. Nearly 70% of the bay’s water is drained during each tide cycle, and in-bay fresh water sources are limited to small perennial streams or direct precipitation via high-rainfall events. Summer upwelling, wintertime downwelling, and in-situ bay biogeochemistry represent significant modes of the observed variability in carbonate dynamics. Summer upwelling is associated with large amplitude diel pCO2 variability, elevated TCO2 and alkalinity, but weak variability in salinity. Wintertime downwelling is associated with bay freshening by both local and remote sources, a strong tidal signature in salinity, TCO2, and alkalinity, with diel pCO2 variability much less amplified when compared to summer. Further, analysis of alkalinity-salinity relationships suggests multiple and discrete water masses inhabiting the bay during one year: mixing of end-members associated with direct precipitation, coastal rivers, southward displacement of the Columbia River plume, California Current surface and deep upwelled waters. The importance of in-bay processes such as net community metabolism during intervals of high productivity are apparent. These direct measurements of pCO2 and TCO2 have proved useful to local hatchery owners who have monitored intake waters following historic seed-production failures related to high-CO2 conditions exacerbated by ocean acidification. Continued monitoring efforts will produce baseline measurements necessary to understand how future warming and ocean acidification will impact our sensitive coastal environments.