The development of GIS based methodologies supports a program for monitoring the territorial dynamics that are occurring in the Estoraos rural watershed (NW Portugal). GIS integrates spatial databases from different research and development projects, with the purpose of understanding: (i) the relationships between land use processes and changes, and environmental management policies; (ii) the extent of environmental impacts due to forest fire as well as extending and intensifying agriculture; and (iii) the influences of natural conditions and human activities on water quality and ecosystem sustainability. The diversity of natural conditions and population dynamics, the (de)forestation, the expansion, density and typology of road networks, the processes of urbanization in the flood plain, and the rising turistic search from external actors, fundament the importance of a GIS based watershed monitoring program. These conditions and processes increase watershed management complexity, namely at a protected wetland in the bottom valley (regional protected landscape, site PTCON00020 of Natura Network 2000, and international RAMSAR site 1613) related to the structure of the landscape, and the quantity and quality of the water resources and the associated biodiversity. The challenges of sustainable land use and the growing quantity and quality of the available spatial databases, allow greater modelling capacity and data accessibility, facilitating public participation, and also aiding and better guiding political and technical actions.