The majority of the Earth’s surface is covered by fine-grained deep-sea sediments, with bacteria dominating total benthic biomass. These benthic bacterial communities depend on organic matter input from the upper ocean, but as they comprise mostly unknown and uncultivated taxa, we have very limited knowledge of their enzymatic machinery to break down this material. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1000 to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA and metagenomic sequencing to elucidate total and active bacterial community composition, and the key functional potentials. Some sequence-dominant taxa of the total community (e.g. members of the Gamma- and Deltaproteobacteria) were underrepresented in the cDNA fraction, while other groups (e.g. Flavobacteriaceae; SAR202 clade) were overrepresented in the active fraction when compared to total community reads. We used the Carbohydrate Active Enzymes database (http://www.cazy.org) to identify protein families in the generated metagenomes, which are associated with polysaccharide degradation, e.g. glycoside hydrolases. We found the same families of glycoside hydrolases in all metagenomes, but their relative contribution to glycoside hydrolase-coding genes varied according to depth. A larger number of hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) was found at shallower depths, while those responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality.