We studied the spatial patterns of the planktonic ecosystems at two Arctic sites strongly affected by Atlantic Inflow (FS, the Fram Strait; and BS, the Barents Sea). A high degree of similarity in the bacterial abundance (mean: 3.1 × 105 cells mL−1 in FS vs. 3.5 × 105 cells mL−1 in BS) was found, while other plankton characteristics were different. Bacterial biomass reached a maximum in BS (3.2–7.9 mgC m−3), while viral abundances tended to be higher in FS (2.0–5.7 × 106 particles mL−1). Larger bacterial cells were found in BS, suggesting the presence of different bacterial populations at both locations. The virus-to-bacteria ratio was significantly higher in FS than in BS (13.5 vs. 4.7). Chlorophyll a concentration was extremely low (<0.25 mg m−3). The highest zooplankton abundance was in the surface layer (919 individuals m−3 in FS vs. 602 ind. m−3 in BS). Zooplankton biomass strongly varied (1–39 mgC m−3), with the maximum in BS. High proportions of boreal taxa in the total zooplankton abundance indicate the Atlantification of pelagic ecosystems in the Arctic. Plankton indicators are correlated with temperature, salinity, and sampling depth. Strong intercorrelations were found between major plankton groups, suggesting tight links in the studied plankton ecosystems.