•A reduction of 50% of the discharge of nitrate from the rivers Mondego e Pranto shown that the has no consequences in terms of trophic activity, reducing the concentrations of nitrate in the estuary, but not the production of phytoplankton. This is a consequence of the limitation growth by the residence time.
•The results have shown also that the “bay behaviour” of the southern channel induces the deposition of particulate organic matter in the channel and the consequent enrichment of the sediments, enhancing the conditions for the development of macro-algae. The growth of these algae is also facilitated by the low values of the velocity. A sensitivity study of the hydrodynamics of that channel to the re-opening of the communication between the channels was performed and it was verified that it clearly modifies the flow.