This dataset contains shipboard Underway conductivity, temperature, and depth (UCDT) measurements taken during the Sub-Mesoscale Ocean Dynamics Experiment (S-MODE) pilot campaign conducted approximately 300 km offshore of San Francisco over two weeks in October 2021. 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 Underway CTD system contains a standard UCDT probe measuring conductivity, temperature, and pressure, as well as an augmented EcoCDT probe that concurrently measures both hydrographic and bio-optical data including conductivity, temperature, pressure, dissolved oxygen concentration, chlorophyll-fluorescence, and particulate backscatter at two different wavelengths. Level 3 data are available in netCDF format with dimensions of profile number and depth.