This dataset contains shipboard conductivity, temperature, and depth (CTD) measurements taken during the Sub-Mesoscale Ocean Dynamics Experiment (S-MODE) field campaign. The experiment was conducted approximately 300 km offshore of San Francisco, during a pilot campaign that spanned two weeks in October 2021, and two intensive operating periods in Fall 2022 and Spring 2023. S-MODE aims to understand how ocean dynamics acting on short spatial scales influence the vertical exchange of physical and biological variables in the ocean. The shipboard CTD rosette is cast from the R/V Oceanus where it records ocean temperature, conductivity, and pressure as it descends to depth and then returns to the surface. IOP1 and IOP2 measurements also contain biological data. Data are available in netCDF format.