This data set comprises 6 files in NetCDF format, containing observational data from two mooring sites, designated as BB and FF, located in the Southern Adriatic Sea. The data covers the period from June 2020 to March 2022. The stand-alone moorings are equipped with Conductivity-Temperature-Depth (CTD) systems that measure biogeochemical properties within the last 100 meters of the water column. These moorings have been configured and maintained for continuous long-term monitoring. As of 2021, the moorings have been integrated into the Southern Adriatic Submarine Observatory of the EMSO-ERIC European Consortium and remain operational. The metadata associated with this dataset comply with EMSO metadata specifications (available at: https://github.com/emso-eric/emso-metadata-specifications/blob/develop/EMSO_metadata.md). The data management plan is detailed in the document titled "Southern Adriatic BB and FF Mooring Data Management Plan for EMSO-ERIC" which can be accessed at https://doi.org/10.5281/zenodo.10412751. The moorings are supported by a grant from Istituto Nazionale di Geofisica e Vulcanologia within the framework of the Joint Research Unit EMSO Italia. This funding is part of the resources allocated by the Italian Ministry of University and Research for international activities related to the European Research Infrastructure EMSO, as well as a grant from the Ufficio Programmazione e Grant Office of CNR-Italy (CNR-UPGO). This version maintains clarity and precision while adhering to scientific conventions.