This study examined total uptake of extracellular polymeric substances (EPS) and glucose and the percentage of prokaryotic cells (Bacteria, Crenarchaea and Euryarchaea) consuming these compounds in the major water masses at the DYFAMED site (NW Mediterranean Sea). The potential assimilation rates of EPS at 10 m depth were higher but on the same order of magnitude as those at 2000 m depth (from 43.4 to 29.0 pmol l−1 h−1). In contrast, glucose assimilation rates decreased with depth from 49.4 to 0.07 pmol l−1 h−1 at 10 and 2000 m depth respectively. Microautoradiography analyses indicated similar percentages of active cells assimilating EPS at 10 and 2000 m depth (13% and 10% of the total-cells). The combination of microautoradiography and catalysed reporter deposition fluorescence in situ hybridization (MICRO-CARD-FISH) analyses revealed that the percentages of Bacteria assimilating 3H-carbohydrates decreased with depth by twofold for EPS. In contrast, the contribution by Euryarchaea to EPS consumption increased with depth by sixfold. At 2000 m, 50% of active cells consuming 3H-carbohydrates were Euryarchaea. These data highlight potential differences in the roles of Bacteria and Archaea in the deep sea biogeochemical cycles and shed light on the importance of deep-sea Euryarchaea in the degradation of dissolved organic matter.