The main aim of this innovative proposal is to provide optimal answers, with the associated uncertainty and risk, to specific management problems in the Guadalquivir estuary (SW Spain). The answers comply with legal, environmental, and socio-economic restrictions. Single- or multi-variable time-series of physical and biogeochemical variables are simulated at tidal, event, seasonal, and multi-annual time scales. The multi-criteria stochastic analysis allows analyzing, for example, different strategies of dredging, regulation of flow rates, drying and flooding of tidal channels and mitigation of the effects of climate change. This multi-criteria approach to estuarine management is, today, an urgent task, given the environmental status of many world estuaries. This is precisely the social challenge facing the PIRATES project.