In the Atlantic Ocean and above the Miami Terrace off southeastern Florida, a total of nine CTD (conductivity, temperature, and depth) casts were performed using the 115-foot Research Vessel (R/V) Weatherbird II above the submerged Miami Terrace at the Miami pockmark and Key Biscayne pockmark from May 4 to May 8, 2016. A CTD is a package of electronic instruments and sampling devices that measure conductivity, temperature, and depth but also capable of measuring multiple chemical and physical parameters of the seawater column. A CTD cast measures the various seawater parameters while the package is lowered and raised in one or more cycles from onboard a ship as it drifts with an ocean current or steams along a predetermined transect. Three casts were performed at Miami pockmark and six at Key Biscayne pockmark: Cast 1 CTD - Miami pockmark, Cast 2 CTD - Key Biscayne pockmark, Cast 3 CTD - Miami pockmark, Cast 4 CTD - Miami pockmark, Cast 5 CTD - Key Biscayne pockmark, Cast 6 CTD - Key Biscayne pockmark, Cast 7 CTD - Key Biscayne pockmark, Cast 8 CTD - Key Biscayne pockmark, and Cast 9 CTD - Key Biscayne pockmark. In addition to conductivity, temperature and depth the following parameters were also measured: oxygen, salinity, nitrogen, turbidity, sound velocity, specific conductance, density, fluorescence. The archived water quality data files, navigation files, and detailed metadata for CTD casts can be downloaded from https://doi.org/10.5066/P9VPA5DW.