This data set includes n.4 files (NetCDF format) containing observational data and related metadata from two mooring sites, sites BB and FF, located in the Southern Adriatic Sea from the period from March 2012 to June 2020. The stand-alone moorings are equipped with an ADCP-RDI system which measures currents along the last 100 meters of the water column and a CTD probe located approximatively 10 m above the bottom. Moorings were configured and maintained for continuous long-term monitoring following the approach of the CIESM Hydrochanges Program (www.ciesm.org/marine/programs/hydrochanges.html). The moorings are currently operational as from 2021 they have joined the southern Adriatic submarine observatory of EMSO-ERIC European Consortium. The data are described in data paper Paladini et al., (In prep): Deep water hydrodynamic observations of two moorings sites on the continental slope of the Southern Adriatic Sea (Mediterranean Sea).