We report on investigations of prokaryotic abundance, biomass, extracellular enzymatic activity, prokaryotic heterotrophic production and respiration in the full water column (∼1200 m) of a deep convection site (the Southern Adriatic Pit), carried out on six cruises in 2006–2008. Prokaryotic abundance (PA) varied vertically and temporally and ranged from 1.2 to 20.4×105 cell ml−1. Cell volumes, generally increased with depth; the lowest mean cell volume was observed in a period with no active convective process (Feb-07) and the highest in a period of stratification (Jun-08) following the convection process occurred in Feb-08. Prokaryotic biomass decreased with the depth and was related with both seasonal cycles of organic matter and hydrological processes. The picophytoplankton ranged in the upper layer (UL) from 0.089 to 10.71×104 cell ml−1. Cells were also recorded till 500 m depth in Feb-08 and this finding could be linked to water convection occurred in the Southern Adriatic Pit in that month. In UL the variations of enzymatic activities as well as leucine-aminopeptidase/ß-glucosidase ratio showed a seasonal trend probably linked to the productive processes of the photic layer. An inverse relation between alkaline phosphatase activity (APA) and phosphate concentrations was found (APA=0.0003PO4−1.7714, R2=0.333, P<0.05). Generally cell-specific enzymatic activities increased with depth as did cell-specific carbon dioxide production rates, while cell-specific prokaryotic heterotrophic production had an opposite trend. High values of prokaryotic growth efficiency registered in the deep layers in Nov-06 reflected a supply of preformed C transported within the deep water masses. Overall, in 2007 when no convective phenomenon was observed, the variability of prokaryotic metabolism was governed by the seasonal cycle of the organic matter, while in Nov-06 and Jun-08 the dynamics of deep water ventilation influenced the trend along the water column of many microbial parameters. The yearly trophic balance of the study site appeared to move towards autotrophy only in UL, whilst in the whole water column, the prokaryotic carbon demand exceeded POC availability rained down from euphotic zone. This mismatch was balanced by the DOC entrapped in the “younger waters” of new formation that alters the normal flux of the biological pump and fuels the deep marine biota in this area of deep water convection.Highlights► In this study we examine the microbiological parameters in a deep convection site. ► We evaluate the variability of carbon flux vehiculated by prokaryotes. ► We find that the deep water convection alters the normal flux of the biological pump. ► The yearly trophic balance appears to move towards autotrophy only in the upper layer. ► We conclude that in the water column the prokaryotic carbon demand exceeds POC availability.