AbstractProkaryotes represent a major fraction of marine biomass and play a key role in the global carbon cycle. We studied the vertical profiles (0–3500 m) of abundance, viability, and activity of prokaryotic communities along a productivity gradient in the subtropical and tropical Atlantic to assess whether there is a vertical linkage between surface productivity regimes and deep ocean prokaryotic communities. We found that latitudinal changes in the vertical patterns of cytometric variables were coupled with surface productivity: higher prokaryotic abundances and viabilities, and smaller cell sizes were observed below highly productive surface waters, an effect reaching down to the bathypelagic layer. Leucine uptake rates in deep waters showed no clear relationship with surface productivity. Changes in resource and energy allocation to growth vs. maintenance in hostile environments, cell‐size‐dependent metabolic requirements, and variability in leucine‐to‐carbon conversion may all be part of the array of factors involved in controlling the prokaryotic activity patterns that were measured. Our work adds to the recent findings that highlight the importance of vertical connectivity for prokaryotic communities in the dark ocean and unveils a remarkable impact of surface conditions in the viability of deep ocean prokaryotes. This is a key aspect when considering metabolic rates of prokaryotic communities in the bathypelagic realm.