The structure of the water column (based on CTD profiles) was assessed in the Southwestern Atlantic (SWA, 36-48ºS, 64-54ºW) during late spring (November 2021) on the Ana Maria Gayoso oceanographic cruise aboard the vessel Bernardo Houssay. The description of the water masses in three regions—the outer Patagonian shelf, the slope waters in the core of the Malvinas Current, and the adjacent open ocean in the Argentine Basin—accompanies the characterization of the protistan plankton and mesozooplankton communities, highlighting the importance of documenting the physico-chemical factors influencing plankton biodiversity.