This dataset contains carbonate system data collected by scientists from the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center to investigate the effects of carbon cycling, coastal and ocean acidification at Crocker Reef located along the Florida Keys Reef Tract, in Southeast Florida, USA. These data were collected using an autonomous instrument called the Ocean Carbon System version 1 (OCSv1) deployed on the seafloor at Crocker Reef. The OCSv1 consists of five sensors integrated into a Sea-Bird Scientific STOR-X submersible data logger including a Seabird SeapHOx sensor for measurement of pH; a Sea-Bird 16 Plus CTD Recorder for measurement of conductivity (for calculation of salinity), temperature, and depth an Aanderaa oxygen optode for measurement of dissolved oxygen; a Pro-Oceanus CO2-Pro for measurement of CO2; and a Wetlabs Eco-PAR sensor for measurement of photosynthetically active radiation. The dataset is a time series of carbonate system parameters including: water temperature (degrees Celsius, °C), pressure (decibar, dbar), salinity, pHT (pH on the total scale), carbon dioxide (parts per million, ppm), pressure from the CO2-Pro Infrared Gas Analyzer (IRGA) (millibars, mbar), dissolved oxygen (milligrams per liter, mg/L) and photosynthetically active radiation (microEinsteins). Each parameter was measured every hour for 24-hour time periods throughout the duration of deployment. Data were collected under Florida Keys National Marine Sanctuary Permit FKNMS-2013-097. For further information regarding data collection and/or processing methods refer to USGS Open-File Report 2019–1003 (https://doi.org/10.3133/ofr20191003).