Despite their exceptional environmental, natural, cultural and economic significance, karstic barrage ecosystems are still poorly investigated. Phytoplankton is an important biological indicator of changes in the ecosystem and accounts for the majority of primary production in freshwater systems, therefore making it useful in assessing the ecological status of water bodies (in accordance with the Water Framework Directive, WFD). Phytoplankton community of Plitvice Lakes, a karstic barrage lake ecosystem, was investigated during a one year period on two vertical profiles (on Lakes Kozjak and Prošće) with the aim of defining the community with similar morphological and functional traits and achieving a better understanding on how the ecosystem is functioning. The research determined how abiotic and biotic factors affected the taxonomic composition of the phytoplankton community. Phytoplankton survival strategies based on the intensity of stress and distortion in the system were determinated. Using different descriptive morpho-functional classifications, the most applicable approach describing phytoplankton community of karstic barrage lakes was defined (in accordance with the WFD instructions), in order to investigate the possibility of using the same approach in determining the ecological status.