We evaluated the relationships between water masses and pico- and nano-phytoplankton and bacterial abundance in the Chukchi Sea. The abundance of picoplankton ranged from 0.01 × 10³ cells.mL^-1 (100 m, station R05) to 2.21 × 10³ cells.mL^-1 (10 m, station R05) and that of nanoplankton ranged from 0.03 × 10³ cells.mL^-1 (100 m, station R07) to 2.21 × 10⁴ cells.mL^-1 (10 m, station R05). The lowest abundance of bacteria in the whole water column (0.21 × 10⁶ cells.mL^-1) was at 100 m at station R17, and the highest (9.61 × 10⁶ cells.mL^-1) was at 10 m at station R09. Melting sea ice affected the physical characteristics of the Chukchi Sea by reducing salinity of the surface mixed layer, resulting in greater hydrodynamic stability of the water column. These changes were accompanied by increased bacterial abundance. The warm Pacific water brought nutrients into the Chukchi Sea, resulting in greater abundance of bacteria and nano-phytoplankton in the Chukchi Sea than in other regions of the Arctic Ocean. However, the abundance of pico-phytoplankton, which was related to chlorophyll a concentration, was higher in Anadyr water than in the other two water masses. The structures of pico- and nanoplankton communities coupled with the water masses in the Chukchi Sea can serve as indicators of the inflow of warm Pacific water into the Chukchi Sea.