Abundance and biomass of pico- (< 2μm) and nanoplankton (2-20μm) were investigated in relation to hydrography during late summer 2006 in Kongsfjorden, Svalbard (79°N, 12°E). Autotrophic and heterotrophic picoplankton abundance ranged from 0.1×10 ⁶ to 35.2 × 10 ⁶ cells L ^-1 and from 0.4×10 ⁶ to 20.3 ×10 ⁶ cells L ^-1, respectively. The highest number of bacteria in the entire water column was recorded at station 2, 10 m (22.3×10 ⁸ cells L ^-1); the lowest value was observed at station 1 (6.0×10 ⁸ cells L ^-1). The abundance of autotrophic and heterotrophic nanoplankton varied from 0.4×10 ⁵ cells L ^-1 to 46×10 ⁵ cells L ^-1, and from 0.3×10 ⁶ to 9.1×10 ⁶ cells L ^-1. Our results demonstrated that heterotrophic nanoflagellates and bacteria in Kongsfjorden microbial community were relatively important followed by statistic analysis. The structure of plankton communities integrated with environmental variables could act as indicators of AW inflow variability in Kongsfjorden.