This zooplankton dataset was collected as part of a larger study examining the effects of hypoxia on species composition, distributions, and predator-prey interactions between zooplankton and fish in a pelagic marine ecosystem. Day/night paired zooplankton sampling was conducted in Hood Canal, Puget Sound (Washington state, US), during 10 monthly cruises from June to October, 2012 and 2013, at five stations: Dabob, Union, Hoodsport, Duckabush and Twanoh. An obliquely towed multi-net system was used to collect depth stratified and full water column samples. For the depth-stratified sampling, depth layers were based on the dissolved oxygen profiles from CTD casts. In the laboratory, zooplankton were quantitatively subsampled and microscopically counted, with zooplankton densities calculated. All individuals were identified to species or larger taxonomic grouping, and by life stages for some species, within each sample. This dataset as published with OBIS incorporates corrections and updates to a dataset previously published on BCO-DMO.