Effects of the sea-ice edge and the Polar Frontal Zone on the distribution of chlorophyll-a levels in the pelagic were investigated during multi-year observations in insufficiently studied and rarely navigable regions of the Barents Sea. Samples were collected at 52 sampling stations combined into 11 oceanographic transects over a Barents Sea water area north of the latitude 75° N during spring 2016, 2018, and 2019. The species composition, abundance and biomass of the phytoplankton community, chlorophyll-a concentrations, hydrological and hydrochemical parameters were analyzed. The annual phytoplankton evolution phase, defined as an early-spring one, was determined throughout the transects. The species composition of the phytoplankton community and low chlorophyll-a levels suggested no phytoplankton blooming in April 2016 and 2019. Not yet started sea-ice melting prevented sympagic (sea-ice-associated) algae from being released into the seawater. In May 2018, ice melting began in the eastern Barents Sea and elevated chlorophyll-a levels were recorded near the ice edge. Chlorophyll-a concentrations substantially differed in waters of different genesis, especially in areas influenced by the Polar Front. The Polar Front separated the more productive Arctic waters with a chlorophyll-a concentration of 1–5 mg/m3 on average from the Atlantic waters where the chlorophyll-a content was an order of magnitude lower.