Abstract Mature ecosystems sequester little organic carbon (C org ) in sediments, as the complex and effective food webs consume most available organic matter within the water column and sediment, in contrast to young systems, where a large proportion of C org is buried in deeper sediment layers. In this paper we hypothesize that “warmer” Atlantic water influenced fjord exhibits the ‘mature’ system features as compared to “cooler” Arctic water influenced fjord. C org concentrations, sources and burial rates, as well as macrobenthic community standing stocks, taxonomic and functional composition and carbon demand, were compared in two west Spitsbergen fjords that are to different extents influenced by Atlantic water and can be treated as representing a cold one (Hornsund) and a warm one (Kongsfjorden). Water, sediments and macrofauna were collected at three stations in the central basin of each fjord. C org , N tot , δ 13 C org and δ 15 N were measured in suspended matter, sediment cores and possible organic matter sources. The composition of sources of sedimentary organic matter was modeled by Mix-SIAR Bayesian stable isotope mixing models. The 210 Pb method was used to calculate sediment accumulation rates, C org accumulation and burial rates. The sedimentary C org concentration and accumulation rate were larger in Hornsund than in Kongsfjorden. The contributions of pelagic sources to the C org in sediments were similar in both fjords, macroalgal detritus had a higher importance in Kongsfjorden, while terrestrial sources were more important in Hornsund. Similar density and species richness were noted in both fjords, but higher biomass, individual biomass, production and carbon demand of benthic communities were noted in Kongsfjorden despite the lower amounts of C org in sediments, indicating that macrobenthos responds to quality rather than quantity of available food. Subsurface tube-building conveyer belt detritus feeders (maldanids and oweniids) were responsible for higher standing stocks and carbon consumption in Kongsfjorden. As a result of the lower C org pool and higher benthic mineralization, the burial rates in Kongsfjorden were much lower (15 g of C org m − 2 yr − 1 ) than in Hornsund (38 g of C org m − 2 yr − 1 ). Our study indicates that warming of the high latitude fjordic environments may reshape the relative proportions of organic carbon sources and induce maturing of the sea bottom systems, in terms of development of stable, biologically accommodated benthic communities which more efficiently mineralize organic matter and consequently lower sequestration of organic matter in deeper sediments.