This data set includes single fish cod data collected during the RV ALKOR cruise AL539 cruise conducted in July 2020 (July 5th to July 18th 2020) in the Western Baltic Sea by the University of Hamburg. The cruise was part of the 5-year MARSYS teaching cruise program of the University of Hamburg GFP20-1_047. All single fish measurements were made directly on board. Full wet weights of cod were measured and subsequently cod were gutted and liver weights, gonad weights and sexes, gutted wet weights (i.e., gutted wet mass), gonad stages and liver nematode infestations were recorded, and Otoliths were taken.