Jellyfish and comb jellies in the Baltic Sea: Depth resolved distribution pattern along the salinity gradient of the Baltic Sea during September 2020 - dataset.

The biodiversity and distribution of gelatinous macrozooplankton was assessed in the Baltic Sea during September 2020. The dataset includes 40,601 species-specific gelatinous macrozooplankton records, representative of 236,329 gelatinous organisms caught across 73 stations in the south-western, central and northern Baltic Sea. Focus was devoted to changes in depth distributions in relation to salinity and an extended oxygen depletion event in the south-western Baltic Sea. In total, 56 Multinet-midi casts (5 depth-strata), 4 Multinet-maxi casts (9 depth-strata), as well as 17 bongo and 52 WP2 casts were performed from the surface to >3 m above the bottom. Data include depth resolved information on the abundance (m and m) and size structure of () the non-indigenous ctenophore - including larvae (1-3 mm), transitional (4-5 mm), young adult (6-9 mm) and adult (≥10 mm) ctenophores, as well as the native scyphozoan jellyfish species ( and (. Additionally, the zooplankton community is described from WP2 nets including species-specific size and biomass data. In total 40,601 individual gelatinous macrozooplankton specimens from samples and sub-samples were analyzed (raw-counts) with 39,771 (corrected-count 235,499), 744 and 86 records. We provide a detailed account of catchability of different life-stages and comparison of different net types. In general, at 89 % of the stations, adult were caught, at an average ( ± SD) density of 1.27 ± 0.97 ind m station (max 8.4 ind m, Flensburg Fjord at 10-7.5m). Young adults were caught at 78 % of the stations with 3 ± 2.4 ind m station (max 29.4 ind m, Eckernförde Bight, south of Flensburg Fjord at 0-2.5 m), but were absent from the northern Arkona Basin and east of Bornholm. At 71 % of the stations, transitional were caught at an average density of 19.2 ± 21.8 ind m station (max 129.2 ind m, WP2, Kiel Bight). Transitional were additionally absent from the central Arkona Basin. larvae were present at 68 % of all stations, with the maximum density observed in Kiel Bight with 642 ind m (WP2). Generally, high larvae densities with >500 ind m were found in the south-western Kiel Bight, with an overall average density of 257 ± 188 ind m. Scyphozoan jellyfish species were found at much lower densities. Maximum abundance of was observed in the Arkona Basin ( 79 at 4 to 6m), with abundances ranging from 0.003 to 1.7 ind m station. was primarily found in the upper 30 m, while was primarily present in waters >30 m (average of 0.002 to 0.07 m). The here presented data are essential to further investigate responses of jellyfish and ctenophores to climate change, especially considering salinity and low oxygen conditions, important global change pressure which are of special concern for the Baltic Sea. Note: The non-indigenous hydromedusae was only found at one station in Kiel Bight, off the Kiel Kanal exit to the SW Baltic Sea ( 1, 8mm, 0.05 ind m).