Abstract: In this paper we examine the use of side scan sonar for estimation and spatial distribution of macrophytes in Arctic conditions. Acoustic observation were verified by video recordings and biological samplings. Single beam echosounder was also used. The Hornsund Fjord represents a periglacial environment with great diversity of morphodynamic processes and sensitivity for global warming changes so it is one of the most promising areas to research the influence of the climate’s impact on ecosystem. Side scan sonar is a very effective and economic tool for mapping marine vegetation on the seafloor but interpretation of data still causes many problems especially in the specific conditions of the Arctic fjords (underwater rocks, postglacial sediments, steep slopes). We have created segmentation and classification algorithm based on the two-dimensional discrete wavelet decomposition of echo signals and fuzzy c-means data clustering. The algorithm was verified using biological data.