Abundance and assemblages of dinoflagellates and ciliates were studied in water samples collected from three different depths at five locations in the Kongsfjorden, during summer (June 14–21, 2011) and fall (September 15–27, 2012). Generally, athecate dinoflagellates were ubiquitously dominant during both seasons. Surface dinoflagellates abundance ranged from 1.87 × 10³ cells/L (KF1) to 11.62 × 10³ cells/L (KF4) and column integrated abundance ranged from 20.3 × 10⁶ cells/m² (KF1) to 126 × 10⁶ cells/m² (KF2) during summer. Dinoflagellate abundance was relatively lower during fall ranging from 0.02 × 10³ cells/L (KF5) to 0.66 × 10³ cells/L (KF3) at surface, and correspondingly, a low column integrated abundance ranging from 2.34 × 10⁶ cells/m² (KF5) to 19.1 × 10⁶ cells/m² (KF1) was observed. Amphidinium sp., Gyrodinium fusiforme, Gyrodinium estuarile dominated during summer, while Gymnodinium sp. was dominant during fall. Among ciliates, aloricate ciliates were more dominant than loricates. Ciliates at surface ranged from as low as 0.069 × 10³ cells/L (KF1) to 3.69 × 10³ cells/L (KF4) during summer. Ciliate abundance increased with depth (up to 20 m). Strombidium spp. (55.28%) and Mesodinium rubrum (36.66%) were dominant during summer. Among the loricates and the aloricates, Strombidium spp. (85.72%) and Tintinnid spp. (92.15%) dominated in fall. The presence of dominant aloricates with characteristic cleptochloroplasts reflected high grazing activity in these waters during both seasons. Diversity study indicates that the dinoflagellates and ciliates are well represented during both seasons. Statistical analyses of the dinoflagellates and ciliates with hydrographic data do not show dominant role of any hydrographical parameters on their diversity, and the same is discussed vis‐à‐vis Atlantification of the fjord.