Amino acids (AA) and carbohydrates (CHO) are important components of the marine organic carbon cycle. Produced mainly by phytoplankton as part of the particulate organic carbon (POC) fraction, these compounds can be released into the outer medium where they become part of the dissolved organic carbon (DOC) pool and are rapidly taken up by heterotrophs (e.g., bacteria). We investigated the quantity and quality of POC and DOC, AA and CHO composition in both pools in three different water masses in the Fram Strait (Arctic Ocean) in summer 2017. Polar Waters and Atlantic Waters showed similar concentrations of particulate and dissolved AA and CHO, despite Polar Waters showing the highest DOC concentrations. In Mixed Waters, where the two water masses mix with each other and with melting sea ice, the concentrations of particulate and dissolved AA and CHO were highest. AA and CHO composition differed substantially between the particulate and dissolved fractions. The particulate fraction (>0.7 μm) was enriched in essential AA and the CHO galactose, xylose/mannose, and muramic acid. In the dissolved fraction non-essential AA, several neutral CHO, and acidic and amino CHO were enriched. We further investigated different size fractions of the particulate matter using a separate size fractionation approach (0.2–0.7 μm, 0.7–10 μm and >10 μm). The chemical composition of the 0.2–0.7 μm size-fraction had a higher contribution of non-essential AA and acidic and amino sugars, setting them apart from the 0.7–10 μm and >10 μm fractions, which showed the same composition. We suggest that the relative differences observed between different size fractions and DOC with regards to AA and CHO composition can be used to evaluate the state of organic matter processing and evaluate the contribution of autotrophic phytoplankton or more heterotrophic biomass. In the future, changing conditions in the Central Arctic Ocean (Atlantification, warming, decreasing ice concentrations) may increase primary production and consequently degradation. The AA and CHO signatures left behind after production and/or degradation processes occurred, could be used as tracers after the fact to infer changes in microbial loop processes and food web interactions.