Mesozooplankton were collected with a MOCNESS net system during the oceanographic cruise JR17005 (May and June 2018) and JR18007 (August 2019). The MOCNESS comprised 9 separate nets which opened in sequence such that the closing of one net opened the next; net 1 was open during the descent of the net to its maximum depth (about 1000 m) while the remaining 8 depths opened at regular intervals during the reascent to the surface. Catches were immediately preserved in 4 percent buffered formaldehyde after division by a Folsom splitter into either 0.5 or 0.25 fractions. Identification of taxa was performed by Continuous Plankton Recorder survey analysts at the Marine Biological Association UK, led by Marianne Wootton. Specimens were categorised to the lowest possible taxonomic level, which, in some cases, encompassed developmental stages but, in other cases, was limited to higher order taxa. Each taxa was enumerated to determine abundance with the preserved fraction of the catch. These were scaled up to the whole catch and divided by the volume filtered of the respective net to determine abundance in units of individuals m-3. These values were also multiplied by the sampled depth interval to derive the alternative unit of individuals m-2. The samples from three net deployments were analysed from both JR17005 and JR18005 in approximately matching locations between Greenland and Svalbard, encompassing the Fram Strait. The dataset allows examination of the distribution and abundance of these species across the region in two separate years, with the first year covering early summer and the second year, late summer. Financial support for was provided by Changing Arctic Ocean (CAO) Programme DIAPOD, funded by UKRI Natural Environment Research Council (NERC; NE/P006213/1, NE/P006353/1, NE/P006302/1, NE/P006183/1,and NE/P005985/1, amongst others), and by CAO Project CHASE, jointly funded by NERC (NE/R012733/1) and the German Federal Ministry of Education and Research (BMBF; 03F0803A).

Mesozooplankton were collected with a motion-compensated Bongo net (61 cm mouth diameter, 100 and 200 micrometre meshes) and a mini- Bongo net (18 cm mouth diameter, 50 micrometre mesh nets). Both nets fished to a maximum depth of 400 m but sometimes shallower. Specimens were categorised to the lowest possible taxonomic level, which in some cases encompassed developmental stages but in other cases was limited to higher order taxa. Each taxa was enumerated to determine abundance in units of individuals m-2. The dataset allows examination of the distribution and abundance of these species within the Atlantic sector of the Southern Ocean over a number of years and covering much of the productive season from spring to autumn. The data for the North Atlantic and Arctic covers one season only (summer) and is limited to providing a spatial perspective on the distribution and abundance of mesozooplankton.

Mesozooplankton were collected with a MOCNESS net system during the oceanographic cruise JR16003 (Dec 2016 to Jan 2017). The MOCNESS comprised 9 separate nets which opened in sequence such that the closing of one net opened the next; net 1 was open during the descent of the net to its maximum depth (1000 m) while the remaining 8 depths opened at regular intervals during the reascent to the surface. All catches were immediately preserved in 4% buffered formaldehyde. Identification of taxa was performed by the Morski Institute (Poland). Specimens were categorised to the lowest possible taxonomic level, which, in some cases, encompassed developmental stages but, in other cases, was limited to higher order taxa. Each taxa was enumerated to determine abundance in units of individuals m-3. The dataset allows examination of the distribution and abundance of these species across Polar Frontal Zone in Southern Ocean Atlantic sector. The survey was funded by The UK Natural Environment Research Council (NERC) and carried out as part of the POETS Wester Core Box and SCOOBIES programmes at British Antarctic Survey. The time of Geraint Tarling and the analysis of the MOCNESS nets was funded by the NERC grant "SeaDNA - Assessing marine biodiversity and structure using environmental DNA: from groundtruthing to food web structure and stability" NE/N00616X/1 PI: Stefano Mariani.