Abstract Due to its high biodiversity the Danube Delta, in Romania, is recognized as a UNESCO World Heritage Natural Site and it is listed as a RAMSAR wetland. The Danube River variable discharges have a great impact on the habitats and the overall ecological status of the delta. One of its most vulnerable parts, from both hydrodynamic and morphological point of view is the Sontea-Fortuna wetland located in the upstream of the Danube Delta. Sontea-Fortuna wetland is susceptible to both floods and droughts. On a long term, decision makers in the area need to know which measures to implement and how these will impact/improve the environment. This article presents how a 3D hydrodynamic model can be used as support for making sound decisions regarding the management of deltaic ecosystems. In particular, the methodology is applied on the Sontea-Fortuna wetland. The case study is part of a wider research in the area, which was developed within the EnviroGRIDS EU FP7 research project. EnviroGRIDS aimed at building capacity for scientists, decision-makers and the general public in the Black Sea Catchment, through collection and sharing of environmental data and models at the basin scale.