This data set comprises all fish biomass data 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. The fish biomass data were collected directly on board. Fish biomass was taken after sorting through a complete fish haul into the single species and weighing them on a scale on board. The amount of Scyphozoa was estimated at 500 kg.