Comau Fjord is a stratified Chilean Patagonian Fjord characterized by a shallow brackish surface layer and a >400 m layer of aragonite-depleted subsurface waters. Despite the energetic burden of low aragonite saturation levels to calcification, Comau Fjord harbours dense populations of cold-water corals (CWC). While this paradox has been attributed to a rich supply of zooplankton, supporting abundance and biomass data are so far lacking. In this study, we investigated the seasonal and diel changes of the zooplankton community over the entire water column. We used a Nansen net (100 µm mesh) to take stratified vertical hauls between the surface and the bottom (0-50-100-200-300-400-450 m). 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. Zooplankton biomass was the highest in summer (209 g dry mass m−2) and the lowest in winter (61 g dry mass m−2). Abundance, however, peaked in spring, suggesting a close correspondence between reproduction and phytoplankton spring blooms (Chl a max. 50.86 mg m−3, 3 m depth). Overall, copepods were the most important group of the total zooplankton community, both in abundance (64–81%) and biovolume (20–70%) followed by mysids and chaetognaths (in terms of biovolume and biomass), and nauplii and Appendicularia (in terms of abundance). Throughout the year, diel changes in the vertical distribution of biomass were found with a daytime maximum in the 100–200 m depth layer and a nighttime maximum in surface waters (0–50 m), associated with the diel vertical migration of the calanoid copepod family Metridinidae. Diel differences in integrated zooplankton abundance, biovolume and biomass were probably due to a high zooplankton patchiness driven by biological processes (e.g., diel vertical migration or predation avoidance), and oceanographic processes (estuarine circulation, tidal mixing or water column stratification). Those factors are considered to be the main drivers of the zooplankton vertical distribution in Comau Fjord.