This dataset contains zooplankton abundance data collected during the RV Dana D1198 cruise in the Northern North Sea, in October 1998. Zooplankton samples were collected using an in situ underwater plankton pump through a 30 µm mesh. The pump was deployed up to 4 times daily and at 8 depths (5, 10, 20, 30, 40, 50, 60 and 80 m) with a pumping time of 3 to 5 minutes in each layer. The nets were carefully washed down, and the contents of the cod ends filtered through a 40 µm mesh. Samples were then preserved in 4% borax buffered formaline sea water for future analysis. These data were collected for the PROcesses of Vertical Exchange in Shelf Seas (PROVESS) project by scientists from the Danish Institute for Fisheries Research (DIFRES). The originator format data are available from: https://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/2bd1b010-66a1-3dc1-e063-7086abc08ac3