The modern Arctic is characterized by a decreased ice cover and significant interannual variability. However, the reaction of the High Arctic ecosystem to such changes is still being determined. This study tested the hypothesis that the key drivers of changes in phytoplankton are the position and intensity of Atlantic water (AW) flow. The research was conducted in August 2017 in the northern part of the Barents Sea and in August 2020 in the Nansen Basin. In 2017, the Nansen Basin was ice covered; in 2020, the Nansen Basin had open water up to 83° N. A comparative analysis of phytoplankton composition, dominant species, abundance, and biomass at the boundary of the ice and open water in the marginal ice zone (MIZ) as well as in the open water was carried out. The total biomass of the phytoplankton in the photic layer of MIZ is one and a half orders of magnitude greater than in open water. In 2017, the maximum abundance and biomass of phytoplankton in the MIZ were formed by cold-water diatoms Thalassiosira spp. (T. gravida, T. rotula, T. hyalina, T. nordenskioeldii), associated with first-year ice. They were confined to the northern shelf of the Barents Sea. The large diatom Porosira glacialis grew intensively in the MIZ of the Nansen Basin under the influence of Atlantic waters. A seasonal thermocline, above which the concentrations of silicon and nitrogen were close to zero, and deep maxima of phytoplankton abundance and biomass were recorded in the open water. Atlantic species—haptophyte Phaeocystis pouchettii and large diatom Eucampia groenlandica—formed these maxima. P. pouchettii were observed in the Nansen Basin in the Atlantic water (AW) flow (2020); E. groenlandica demonstrated a high biomass (4848 mg m−3, 179.5 mg C m−3) in the Franz Victoria trench (2017). Such high biomass of this species in the northern Barents Sea shelf has not been observed before. The variability of the phytoplankton composition and biomass in the Franz Victoria trench and in the Nansen Basin is related to the intensity of the AW, which comes from the Frame Strait as the Atlantic Water Boundary Current.