Fjords in the high Arctic, as aquatic critical zones at the interface of land-ocean continuum, are undergoing rapid changes due to glacier retreat and climate warming. Yet, little is known about the biogeochemical processes in the Arctic fjords. We measured the nutrients and the optical properties of dissolved organic matter (DOM) in both seawater and sediment pore water, along with the remote sensing data of the ocean surface, from three West Svalbard fjords. A cross-fjord comparison of fluorescence fingerprints together with downcore trends of salinity, Cl−, and PO43− revealed higher impact of terrestrial inputs (fluorescence index: ~1.2–1.5 in seawaters) and glaciofluvial runoffs (salinity: ~31.4 ± 2.4 psu in pore waters) to the southern fjord of Hornsund as compared to the northern fjords of Isfjorden and Van Mijenfjorden, tallying with heavier annual runoff to the southern fjord of Hornsund. Extremely high levels of protein-like fluorescence (up to ~4.5 RU) were observed at the partially sea ice-covered fjords in summer, in line with near-ubiquity ice-edge blooms observed in the Arctic. The results reflect an ongoing or post-phytoplankton bloom, which is also supported by the higher levels of chlorophyll a fluorescence at the ocean surface, the very high apparent oxygen utilization through the water column, and the nutrient drawdown at the ocean surface. Meanwhile, a characteristic elongated fluorescence fingerprint was observed in the fjords, presumably produced by ice-edge blooms in the Arctic ecosystems. Furthermore, alkalinity and the humic-like peaks showed a general downcore accumulation trend, which implies the production of humic-like DOM via a biological pathway also in the glaciomarine sediments from the Arctic fjords.