UNDER EMBARGO - This dataset is part of BE/2023 sampling campagn in SW Greenland fjords (Igaliku and Tunulliarfik). The dataset reports the final concentrations (μg L⁻¹) of each detected photosynthetic pigment, used to infer phytoplankton functional groups and compare community composition across fjords with differing glacial influence and between seasons (spring–summer). For pigment analysis, seawater volumes ranging from 700 mL to 1 L were filtered onto 25-mm diameter Whatman GF/F filters and immediately stored at -80°C until further analysis. Pigments were extracted using 90% acetone and analysed by High-Performance Liquid Chromatography (HPLC) following the method of Van Heukelem and Thomas (2001). Calibration was performed using pigment standards from DHI Water and Environment (Hørsholm, Denmark). In the dataset is indicated the final consentration (μg/L) of each detected photosyntetic pigment.