Implementation of the European Water Framework Directive is one of key issues for every EU member state country. Therefore efforts are taken to make good assessment systems of ecological status for each water body. The aim of this study was to investigate is there phytoplankton community in Croatian lowland rivers and is it suitable to use it as one of five biological elements for assessment of ecological status. For that purpose, HRPI index (Hungarian River Potamoplankton Index) was applied and ecological status was compared with chemical status of water. Chemical and physical properties of water, together with average monthly discharge were analyzed together with phytoplankton biomass in four investigated rivers (Mura, Drava, Danube and Sava) on nine sampling sites from April till September of 2010. Nutrients in form of nitrogen ions and water discharge was confirmed to be one of the main driving factors for phytoplankton community in large lowland rivers. Functional group concept, already showed as good descriptor of phytoplankton community in lowland Pannonian rivers, was demonstrated here as well as good indicator of human impact and good basis for assessment of ecological status in large lowland rivers. Dominant codons of functional groups that represents Bacillariophyceae were C, D and TB and codon T that represents Chlorophyceae. This research showed successful application of HRPI in Croatian lowland rivers and its results were followed by ecological status based on physical and chemical properties of the water. Ecological status of large lowland rivers in Croatia was evaluated as good.