Seasonal, diel and vertical distribution of mesozooplankton was described over the entire water column of Comau Fjord, northern Chilean Patagonia. Stratified vertical hauls we taken with a Nansen net (100 μm mesh) between the surface and the bottom (0-50-100-200-300-400-450 m) in spring, summer, autumn and winter. Samples were scanned with a ZooScan, and abundance, biovolume and biomass were determined for 41 taxa identified on the web-based platform EcoTaxa 2.0. This dataset was generated in the frame of the co-operation between the Universidad Austral de Chile (https://www.uach.cl), the Huinay Scientific Field Station (http://www.huinay.cl) and the Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research (http://www.awi.de) in the frame of the project PACOC Plankton- And cold-water COral ecology in Comau Fjord, Chile. The study was also embedded in activities of the Research Center Dynamics of High Latitude Marine Ecosystems (IDEAL) (http://www.centroideal.cl/eng/).