Fjords of West Spitsbergen are very dynamic in terms of hydrology. Here we tested whether the qualitative analysis of the taxonomic composition of phytoplankton may be useful as a fast method to assess the origin of the waters and whether it can give any additional information to hydrological data. Phytoplankton samples were collected along transects in Hornsund and Kongsfjord. Among total of 109 taxa identified, only 49 were common in both fjords. The assemblages in Hornsund implied that inflow of the cold waters of the Sřrkapp Current had occurred some time before samples collection, while in Kongsfjord the taxonomic composition was typical for the summer and did not show any recent, unusual hydrological phenomenon. Concluding, the method can be useful in the surveys in which hydrological data are collected infrequently.