Raw physical oceanography data acquired during research cruise MSM96 on RV MARIA S MERIAN. This expedition was conducted in the North East Atlantic Ocean at two work sites (PAP: Porcupine Abyssal Plain, IAP: Iberian Abyssal Plain) to assess the natural heterogeneity of seafloor characteristics and sediment geochemistry. Cruise MSM96 operated in October and November 2020.CTD data was acquired by the ship-based hydrocast CTD (AWI Sensor Information URN: vessel:maria_s_merian:sbe_911plus_merian, GEOMAR equipment id: MSM_ENV-1_CTD_Seabird911Plus) to provide salinity and temperature data for sediment geochemistry analyses. Only deployment MSM96_67-1_CTD successfully reached the seafloor with the CTD readings intact. All other deployments had sensor failure, roughly below 2000m.