The study operationalized the HELCOM core indicator “Zooplankton mean size and total stock” (MSTS) in the Western Baltic Sea. The indicator is also used under the Marine Strategy Framework Directive to assess food webs and pelagic habitats. On the basis of a monthly data collection 2015-2016 in Kiel Bay, Bay of Mecklenburg, Arkona and Bornholm Basin it was investigated whether, on the basis of the seasonal occurrence, interannual or sampling variability of indicator-relevant zooplankton taxa the current monitoring strategy is sufficient to assess the indicator. On the basis of a long-term data series reference periods were derived with respect to eutrophication and fish nutrition and an assessment of the indicator was carried out.