The Central Adriatic Sea is characterized by three depressions collectively known as Pomo (or Jabuka in Croatian) Pits, with a maximum depth of about 270 m (Marini et al 2016) and bottom mainly composed of fine muddy sediment (Trincardi et al. 2014). The Middle Adriatic Deep Water (MAdDW) dwelling within the Pomo Pits is renewed at intervals of one to three years or occasionally longer, as a result of the formation of the Northern Adriatic Dense Water (NAdDW) (Vilibić 2003; Marini et al 2016). In addition to being characterized by a very peculiar bathymetry and oceanographic characteristics, this area hosts one of the main nursery for the European hake Merluccius merluccius within the Northern and Central Adriatic Sea (Angelini et al. 2016) and a population of Nephrops norvegicus, characterized by small-sized mature individuals (Angelini et al. 2020); furthermore, this area historically represented one of the main fishing ground shared by Italian and Croatian fleets targeting both species, which showed a decline in landing in the last decades (Russo et al. 2018; FAO‐GFCM 2021). After a series of management measures implemented since 2015 by the Italian and Croatian governments, the General Fisheries Commission for the Mediterranean established in 2018 the Pomo Pits Fishery Restricted Area (GFCM 2017) and recently confirmed its permanent duration (GFCM 2021).  In the framework of an agreement with the Italian Ministry of Agriculture and Forestry (MIPAAF), CNR-IRBIM carries out since 2015, on board R/V Dallaporta, an autumn trawl survey in the western side of the Pomo Pits area; the survey aims to evaluate the effects of the management measures enforced in the area on the most commercially and ecologically important species (ScamPo survey; Martinelli et al. 2021). Furthremore, to understand possible effects of environmental changes on the species abundance and distribution, before or after each trawl haul, CTD (Conductivity Temperature Depth) data are collected with a SeaBird Electronic SBE 911plus (years 2015-2019) and SeaBird Electronic SBE 19plusV2 (years 2020 and 2021). The multi-parameter probes are also equipped with a SBE43 dissolved oxygen (concentration and saturation) sensor. A SBE 5T pump ensures a constant flow over time inside the sensors. The dataset here presented contains 61 CTD and Oxygen averaged profiles (0.5 db pressure interval) collected in autumn (from 2015 to 2021) within the Pomo Pits and in the surrounding area by means of multi parametric probes.  All the profiles were subjected to quality control. Data are flagged according the L20 (SEADATANET MEASURAND QUALIFIER FLAGS).