This dataset contains the CTD data were collected during the PIAF project (Fish inventory using environmental DNA), between 30/04/2023 and 11/05/2023, around Corsica, western Mediterranean, jointly by the Andromède océanologie [https://www.andromede-ocean.com/] (France) and MARBEC MARine Biodiversity, Exploitation and Conservation [http://www.umr-marbec.fr/en/?lang=en] (France) teams. The CTD data were obtained using RBR concerto3 autonomous logger from Victoria IV trimaran belonging to Scopra, France and chartered by the University of Montpellier. 79 transects (16 were 2.5-km long and 63 were 5-km long) were performed along the -40m isobath (34,6 m in mean, 5 m above the seabed in mean), i.e. the lower limit of the Posidonia meadow, east, south and west Corsica between latitude 41.2-43°N and longitude 8.4-9.5°E. The sensors measured and recorded conductivity (mS/cm), temperature (°C), pressure (dBar), dissolved O2 concentration (µmol/L) and turbidity (NTU). Other parameters were derived from the previous measurements: sea pressure (dbar) removing atmospheric pressure, depth (m) simplifying and using density parameter, salinity (PSU) or Practical Salinity Scale (PSS-78), speed of sound (m/s) based on UNESCO algorithm, specific conductivity (µS/cm) and dissolved O2 saturation (%). All parameters were measured or calculated at depths ranging from -5 m to -49 m (Table 1). Recordings were made every 0.5 seconds (2 Hz frequency). The accuracy, specified by the manufacturer, were ±0.003mS/cm for conductivity, ±0.002°C for temperature, ±0,1 dbar for pressure (Depth), a maximum of ±2μmol/L or ±1.5% for dissolved O2 concentration and saturation.  RBR Concerto3 was factory calibrated before. The downloadable files are a csv of CTD probe data, a geopackage with the spatialized transects and a folder with a pdf showing the evolution of all the variables, accompanied by a text explaining the methodology and the meteorological parameters that influenced the measurements.