The paper presents the results of studies of nanophytoplankton in the fjords of Western Spitsbergen in the summer of 2001, 2002, 2003 and 2017. It is shown that the water area of each fjord is characterized by a fragmentation of the community of planktonic nanoalgae with depth and from the apex to the mouth region, as well as a deepening of the core of maximum abundance at the exit from the fjord, regardless of the density structure of the water column. For fjords of different latitudinal locations, a decline in integral indicators, a lowering of the community core from the surface horizon, and the replacement of large size fractions by cells smaller than 5 μm in the northern direction as the water temperature increases were recorded. In terms of interannual variability, the total abundance and structural organization of nanophytoplankton were determined by the degree of temperature stratification. In the summer of 2017 an increase in the absolute values of abundance and biomass by 1–2 orders of magnitude compared to zero years was revealed, while maintaining the main features of the structural organization of the community.