The absorption of carbon dioxide into the ocean acidifies the waters and has the potential to drastically alter the chemistry upon which organisms and ecosystems depend. This effect, however, is expected to vary between water masses that already differ in terms of their existing carbonate chemistry. The San Juan Archipelago is an ever-changing, complex estuarine ecosystem with little published literature regarding spatial and temporal variation in its carbonate chemistry. After measuring DIC and TA between the neap and spring tide at nine locations throughout the archipelago, we found that the water differs through space and time – both throughout the monthly tidal cycle as well as the daily tidal cycle. Measurements for six parameters – salinity, temperature, DIC, TA, pCO2 and pH – were analyzed to further understand how areas that experience low, medium and high amounts of flushing over the tidal cycle may differ in their water chemistry. Due to few replicates and insufficient sampling days, we were only able to conclude that the Fraser River, tides and likely biology all impact the carbonate chemistry of the region. We hope that further studies will be conducted in the region to better quantify how well it will withstand increasing ocean acidification.