A large amount of ocean heat and carbon is transported northward through the Florida Straits, the upper limb of the Atlantic Meridional Circulation, and plays a role in ocean carbonate chemistry along the U.S. east coast. Our understanding of carbon transport and ocean acidification in the Florida Straits is limited by insufficient carbonate chemistry data within this region. To address this issue, we developed an algorithm based on high-quality data from carbonate chemistry-focused research cruises. Then we applied this algorithm to seasonally resolved hydrographic time-series data from 2002 to 2018 to generate the carbonate chemistry datasets for the study region. We found that short-term variation in surface water dissolved oxygen was strongly correlated with volume transport. During the past two decades, dissolved oxygen showed a significant decreasing trend, and dissolved inorganic carbon showed a significant increasing trend. In addition, the increasing rate of dissolved inorganic carbon was highest in North Atlantic Central Water where the decreasing rate in dissolved oxygen was greatest. Furthermore, the long-term declines in pH and aragonite saturation state have the potential to threaten the health of corals living in the Florida Straits.