UNDER EMBARGO - This dataset is part of BE/2023 sampling campagn in SW Greenland fjords (Igaliku and Tunulliarfik). Pelagic community was analysed using Imaging Flow Cytometry (iFCM) with an ImageStream®X Mk II. Cells were grouped into functional size classes—pico-, nano- and microplankton—according to measured cell length. Cells lacking chlorophyll autofluorescence were classified as heterotrophic or chemotrophic organisms, including heterotrophic picoplankton/bacteria (HP; ≤2 µm) and heterotrophic nanoplankton (HN; 2–20 µm). No larger heterotrophs (>20 µm) were visually detected. Autofluorescent cells were considered phototrophic, although this fraction may also include mixotrophic taxa, and comprised picophytoplankton (AP; ≤2 µm), nanophytoplankton (AN; 2–20 µm), and microphytoplankton (AMicro; 20–100 µm). To estimate the biovolume of each plankton class, the two-dimensional cell surface area measured by the IDEAS® imaging software was multiplied by the mean cell width, assuming that cell width approximates the third spatial dimension. Carbon biomass was subsequently derived from biovolume using established carbon–volume relationships. For the HP fraction, carbon content was estimated using the bacterial conversion proposed by Romanova and Sazhin (2010), where volume is expressed in µm³. Although the HP fraction may also include heterotrophic picoeukaryotes, and its biomass may therefore be partly underestimated, this conversion was applied because the fraction was assumed to be numerically dominated by bacteria. For the other protist groups, carbon biomass was derived following Menden-Deuer and Lessard (2000). Carbon values were converted from pg C cell⁻¹ to carbon biomass (µg C L⁻¹) based on cell abundance.