Phytoplankton species distribution and composition were determined by using microscopy and pigment ratios in the Kongsfjorden during early autumn 2012. Variation in sea surface temperature (SST) was minimal and matched well with satellite-derived SST. Nutrients were generally limited. Surface phytoplankton abundance ranged from 0.21 × 10(3) to 10.28 × 10(3) cells L(-1). Phytoplankton abundance decreased with depth and did not show any significant correlation with chlorophyll a (chl a). Column-integrated phytoplankton cell counts (PCC) ranged from 94.3 × 10(6) cells m(-2) (Kf4) to 13.7 × 10(6) cells m(-2) (Kf5), while chl a was lowest at inner part of the fjord (6.3 mg m(-2)) and highest towards the mouth (24.83 mg m(-2)). Biomass from prymnesiophytes and raphidophytes dominated at surface and 10 m, respectively. The contribution of Bacillariophyceae to biomass was low. Generally, heterotrophic dinoflagellates were great in abundance (12.82 %) and ubiquitous in nature and were major contributors to biomass. Various chl pigments (chl b, chl c, phaeopigments (phaeo)) were measured to obtain pigment/chl a ratios to ascertain phytoplankton composition. Phaeo were observed only in inner fjord. Chl b:a ratios and microscopic observations indicated dominance of Chlorophyceae at greater depths than surface. Furthermore, microscopic observations confirmed dominance of chl c containing algae throughout the fjord. The study indicates that pigment ratios can be used as a tool for preliminary identification of major phytoplankton groups. However, under the presence of a large number of heterotrophic dinoflagellates such as Gymnodinium sp. and Gyrodinium sp., pigment signatures need to be supplemented by microscopic observations.

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.

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