Arctic fjords are hotspot for organic matter (OM) transformation and storage, however, the composition and sources of the particulate organic matter (POM) are still not completely understood. Further, due to the ongoing enhancement in the glacier melting, runoff, and precipitation, the coastal Arctic is expecting considerable increase in POM inputs. Therefore, we investigated the biochemical composition of the POM through the application of stable isotopes, C:N ratio, and biomolecules, across different regions and depths in Kongsfjorden (Svalbard) during the late-summer. We observed that Kongsfjorden-POM was characterized by low δ13C (−29.0 to −26.7 ‰) with similar values at different locations (inner to outer) of the fjord at each depth. However, C:N ratio showed increasing trend (5.7 to 10.9) from outer to inner fjord indicating marine to terrestrial transition. Monosaccharide distribution (such as fucose, galactose, arabinose, xylose, ribose, and rhamnose) and their diagnostic ratios supported the marine versus terrestrial gradient in the POM characteristics in the surface water across the fjord. Only the outermost station showed consistent biochemical distribution indicative of phytoplanktonic sources in the POM, while the rest of the fjord showed mixed signatures of marine and terrestrial sources. Higher abundance of mannuronic acid (26.6–50.8 mol%) at the middle and bottom depths highlighted possible macroalgal contribution to the POM. The stratified surface water had a relatively higher (0.5–2 ‰) δ13C and carbohydrates (40–65 μg/L) than the middle and bottom depths, with a strong positive correlation between δ13C and particulate carbohydrates, indicating a stratification-induced distribution of POM. The study showed the importance of non-phytoplanktonic OM sources, such as terrestrial, freshwater and macroalgae POM in the fjord water column, and the fate of labile (carbohydrates) fraction that predominates in stratified surface waters. Therefore, the future warm and wet Arctic will most likely lead to changes in the fate of the organic matter in the fjord water.