In Portugal, from the beginning of the 20(th) century to the 1970s water management was regarded a non-integrated activity. Various hydraulics projects were developed in the country with the main objective of making an inventory of works that should be undertaken to develop important economic sectors. In that context, the energy and agricultural sectors were considered the most relevant. These plans were developed within a water policy that set hydraulic works above environmental concerns. Regulations published at the beginning of the 1980s established a consistent legal target for water management for the first time in Portugal. The newly-introduced concepts and regulations established provided for the creation of an interface with users, the preparation of reports and field information about water use proposals and hydrographic network changes. The existing regulations in Portugal attributes the Water Resources Planning per Hydrographic Basin and establishes the contents of the above-mentioned plans. All the Hydrographic Basin Plans in Portugal have been concluded recently. These plans are structured around five main systems: environmental, socioeconomic, infra-structural, institutional and financial-fiscal. The systematization, interpretation and information exchange referring to each of these systems are the development pillars underpinning the Hydrographic Basin Plans (HBPs). Since 1999, pollution has been partially alleviated and water quality is slowly improving, now that a different strategy and regulation for water management has been introduced. As a first step towards improvement, water prices and charges for sewage treatment should be markedly increased for all users, very soon. Also, as a general consequence of the approved HBPs, new strategies and specific programs for safeguarding and improving water resources should be designed and implemented. Different environmental problems have been detected during the diagnosis phase of some HBPs and these need to be solved urgently, within an integrated management concept. Among them we can highlight: dam-reservoir systems, intensive agriculture and pig farming, inadequate water quality, environmental degradation in cities and flood hazards in the main courses. This paper presents and systematizes the main development phases of one Program that has been submitted and undertaken, and which is currently being implemented in three specific case-studies (the Portuguese Mondego, Vouga and Lis rivers and estuaries). It is regarded as a highly innovative Program because of the following interrelated aspects: it adopts the systems approach; it is oriented towards new goals of environmental management; it involves a new combination of disciplines; it indicates new strategies for collecting indicators; it proposes new, concrete, empirically measurable indices for sustainable development; it is likely to develop new indicators, and it should provide new tools.