This dataset contains shipboard Underway conductivity, temperature, and depth (UCDT) 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 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. The level 2 data herein combines measurements from both the UCDT and EcoCDT into a single dataset, where for each variable, all profiles are binned onto a 5m vertical grid and merged into a 2-D matrix. Additional computed variables include backscatter baseline signal and backscatter spike signal. Data are available in netCDF format.