This dataset contains carbon dioxide (CO2) system data collected by scientists from the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center (SPCMSC) to investigate the effects of Mercuric chloride (HgCl2) on low salinity, organic-rich estuarine water samples acquired from the Tampa Bay estuary located in west central Florida. Discrete water samples were collected using two, 30-liter (30L) Niskin bottles to capture surficial waters from the lower Hillsborough River. Filtered water samples collected from one Niskin bottle were "poisoned" with HgCl2 (according to best practices (Dickson and others, 2007), while filtered water samples collected from the second Niskin were left "as is" (unpoisoned) to act as the experimental control. Water samples were analyzed incrementally over a period of three months at the USGS Carbon Analytical Laboratory in St. Petersburg, Florida. This dataset contains the elapsed time experimental results of CO2 system parameters including water temperature (Celsius, C), salinity, pHT (pH on the total scale), total alkalinity (AT, micromoles/kg), and total dissolved inorganic carbon (CT, micromoles/kg). For further information regarding data collection and/or processing methods, please refer to the associated journal publication (Moore and others, 2023), which is based on a thesis publication by Moore and others (2021).