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Knowledge on ecosystem functioning can largely contribute to promote ecosystem-based management and its application. The Mar Piccolo of Taranto is a densely populated area at a high risk of environmental crisis. Here, planktonic primary production (PP) and heterotrophic prokaryotic production (HPP) were measured as proxies of functioning in three sampling sites located in two inlets at different levels of industrial contamination, during three sampling surveys (June 2013, February and April 2014). To have a better overall view and provide some insights into the benthic-pelagic coupling, we integrated PP and HPP in the water column with those in the sediments and then discussed this with the origin of the organic matter pools based on analysis of stable isotopes. Heavy metals and polychlorobiphenyls (PCBs) were also analysed in the surface (1 cm) sediment layer and related to the overall ecosystem functioning. Multidimensional scaling (MDS) analysis, based on the main data, clearly separated the second inlet from the first one, more severely impacted by anthropogenic activities. The stable isotope mixing model suggested the prevalent terrestrial/riverine origin of the particulate organic matter pools (mean 45.5 %) in all sampling periods, whereas phytoplankton contributed up to 29 % in February. Planktonic PP and HPP rates followed the same pattern over the entire study period and seemed to respond to phytoplankton dynamics confirming this community as the main driver for the C cycling in the water column. On the contrary, benthic PP rates were almost negligible while HPP rates were lower or comparable to those in the water column indicating that although the Mar Piccolo is very shallow, the water column is much more productive than the surface sediments. The sediment resuspension is likely responsible for a pulsed input of contaminants into the water column. However, their interference with the proper functioning of the pelagic ecosystem seems to be limited to the bottom layers.