In 2011, zooplankton community structure was investigated in a set of 16 locations on the Danube river and shallow lakes in the Danube delta, between September 27 and October 04. Three partner countries were involved in the sampling programme: Romania (RO), Ukraine (UA), Moldova (MD); each country collected one sample following its own ‘national’ sampling methodology. This study provides details on zooplankton community structure and surface water quality using saprobic index as an indicator. The overall objective of the study is to complement the activities of the International Commission for the Protection of the Danube River (ICPDR) required to strengthen a regional approach for solving transboundary problems. The comparison of the dataset gathered is useful to test the hypothesis that reported species and methodologies used are useful for water quality assessment. The result showed that the zooplankton species are important indicators of the trophic state in Danube Delta aquatic ecosystems.