This dataset provides abundance data for meiofauna taxa determined from sediment samples collected in the Weddell Sea (mostly South-Eastern). A minimum of three samples (cores) were collected at each station with a MUC10 multicorer or taken from a giant box corer during PS96. Sediment cores were sliced into depth layers (stations 017, 026, 061, 072: 0–2cm, 2–5cm, 5– bottom; stations 001, 037, 048: 0–1cm, 1–2cm, 2–3cm, 3–4cm, 4–5cm, 5– bottom) and preserved in 4%-borax-buffered formaldehyde solution prior to sieving (upper sieve size 500 µm, lower sieve size 32 µm) and counting (detailed methods in Säring et al. submitted). Abundance is presented per depth layer from the top 5 cm (note different slice volume) as ind./10 cm². Meiofauna communities included individuals from 22 higher taxa. The meiofauna abundance data are part of a larger ecological study on meio- and macrofauna communities and their relation to environmental conditions and remineralisation at the sediment-water interface (see “Related to” below). For the larger study, sediment cores from which meiofauna abundance data are deposited here were also used for microcosm incubations: Untreated incubations (Benthic ecosystem Function Experiments BEFEx), and incubations with and without microalgae addition (Algae Feeding Experiment AFEx). Cores from BEFEx and AFEx without algae are labeled with NT (not treated), cores from AFEx with algae are labeled as T (treated).