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The Mar Menor lagoon has been subjected to high anthropogenic pressures. Among them, in the early 1970s, dredging and enlargement of one of the inlets to make a navigable channel has had strong consequences on the hydrology, ecology, and fisheries of the lagoon. In recent years, changes in agricultural practices have induced an eutrophication process, leading to loss of water quality. As a solution, some management proposals have included dredging of the inlets in order to increase the water renewal. However, these proposals did not take into account the negative effects of previous experiences nor the consequences on environmental conditions of the lagoon and therefore on biological processes. The purpose of this work is to assess the effect that proposed mitigation measures, could have on the hydrodynamic conditions and discuss its possible ecological consequences. A three-dimensional (3D) numerical model has been used to simulate the lagoon under different dredging scenarios, covering different dredging depths and extensions. The simulated current fields and fluxes through the inlets, as well as water renewal times have been compared for the different scenarios. It is found that some of the considered scenarios take the system beyond the threshold of sustainability, where the modified current dynamics could affect sediment transport, beach dynamics and fishing capacities in a significant way. Water exchange with the Mediterranean is also strongly affected, with consequences for species connectivity, and a homogenization of the water renewal times that could lead to loss of ecosystem heterogeneity and structural complexity. The study demonstrates the utility of numerical models as effective tools for the management of coastal areas.