When located within estuarine surroundings, Natura 2000 areas are often more vulnerable to the impacts, not only from man-made pressures, but also, from complex climatic, hydrodynamic and geomorphological factors, and often call for public intervention for protection. Among the various instruments of environmental policy to safeguard environmental values, public expenditure dedicated to protect and restore particular places and associated economic and environmental functions, as well as to minimize risks, may be critical. In 2008, the Portuguese Government initiated a national policy program for the protection of coastal and estuarine areas. Under its aegis, three specific integrated interventions of approximately €100M each were dedicated to three areas - “Ria Formosa”, “Ria de Aveiro”, “Litoral Norte”. It was expected that, through the implementation of multiple projects, the integrated interventions would allow significant investment in 151 km of seashore, 220 miles of estuarine banks, in order to enhance environmental resources, seen as competitive factors within each respective economic region, to protect and improve environmental factors, to prevent and protect people and assets from natural hazards and to ensure conditions for public enjoyment of environmental values. The financial crisis in the country as well as the government change in the middle of 2011, however, has threatened the implementation of these programs. This paper assesses the impacts emerging from the financial crisis on the implementation of these programs, through three main levels - the environmental level focusing on the impacts over the reduction of recovery of environmental values and consequent implementation of Nature 2000 network objectives, the economic level focusing on the loss of opportunity to improve conditions for natural resources economic based activities, and the institutional level focuses on the trust relationships between national state level and the municipalities, established with so much effort and enthusiasm for the promotion of the programs.