This dataset shows the relative abundance of the five most important open ocean and sea ice indicator ASVs for the time interval 5–45 kyr b2k in GS16-204-22CC-B, Eirik Drift, Labrador Sea. The open ocean indicator ASVs are identified in the Holocene (5–8 ky b2k); the sea ice indicator ASVs in MIS 2-3 (20–35 ky b2k) of GS16-204-22CC-B. In these calibration windows, the indicator ASVs cannot be used for interpreting the environment. The indicator ASVs were identified in our metabarcoding dataset via the multipatt function of the indicspecies v1.8.0 R package (Cáceres and Legendre, 2009). The full metabarcoding dataset is available from the European Nucleotide Archive repository via accession number PRJEB112075.