Estuarine and coastal areas have been intensively studied given their complexity, ecological, and societal value and the importance of their ecosystem services. Estuarine and coastal management must be based on a sound characterization of these areas, which is achievable complementing the comprehensive field measurements with numerical models solutions. Based on a detailed comparison between two close-by, but extremely different, Portuguese estuaries (the Douro and Minho estuaries), this chapter intends to discuss how accurately numerical modeling tools can provide relevant information for a variety of coastal zones. They can be very useful for various applications in the planning and management fields, such as coastal and infrastructures protection, harbor activities, fisheries, tourism, and coastal population safety, thus supporting an effective and integrated estuarine and coastal management, which must consider both the safety of the populations and the sustainability of the marine ecosystems and services. In particular, the capacity of the numerical models to give a detailed characterization of morpho-hydrodynamic processes, as well as assess and predict the effects of anthropogenic interventions, extreme events and climate change effects, are presented.