This dataset contains in-situ seawater samples taken during the Sub-Mesoscale Ocean Dynamics Experiment (S-MODE) conducted approximately 300 km offshore of San Francisco during a pilot campaign over two weeks in October 2021, and two intensive operating periods (IOPs) 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. Water samples collected in Niskin bottles mounted on the ship’s rosette sampler were taken of chlorophyll (µg/L), phaeopigments (µg/L), and nutrient concentrations (µM or µmol/L) of particulate organic carbon, particulate organic nitrogen, silicate, nitrate, nitrite, and phosphate. Samples analyzed with fluorometry contain chlorophyll concentrations in µg/L and phaeopigment concentrations in µg/L. Samples analyzed with elemental analysis contain POC molarity in µM and PON molarity in µM. Samples analyzed via ion analysis contain silicate concentrations in µM, total nitrate+nitrite in µM, phosphate in µM, nitrite in µM, and nitrate in µM. These data are mainly used by S-MODE for validating the PRISM-derived products and calibrating the in-situ sensors on the autonomous platforms. Data are available in netCDF format.