Methods to evaluate river ecosystems for conservation purposes have improved substantially during the last 20 years, but habitat degradation and losses of freshwater biodiversity have accelerated over this period. Traditional approaches for assessing conservation status are unsatisfactory because they are largely based on the risk of extinction of endangered species and habitats. This chapter presents a more comprehensive way of assessing conservation status, using as examples alder-ash Alnus glutinosa-Fraxinus excelsior alluvial forest habitat and Atlantic salmon Salmo salar in the Natura 2000 river network of the Cantabria region in northern Spain. The assessment uses specific indicators such as distribution range, population structure and vulnerability to human activities to establish whether a habitat or species is achieving favourable conservation status. Information for these indicators is derived from a variety of map-based and field survey data, historical information and future scenarios. Several assumptions are made about rule-based criteria that determine specific and overall indicators of status.Although alder-ash alluvial forest is relatively widespread, its status is assessed as ‘inadequate’ in more than 20% of surveyed areas and the habitat is considered ‘vulnerable’ in more than two-thirds of the river network. The distribution range of Atlantic salmon has been severely reduced in all but two rivers, and its population structure and composition are considered inadequate for all the study rivers which are also highly vulnerable to several human activities. The conclusion is that the current conservation status is inadequate for all Cantabrian salmon populations.Our method needs to be tested further, particularly in relation to the need for more reliable information about ‘reference conditions’, but it does represent a promising improvement on the much narrower focus of the current assessment of conservation status. The use of modern technology and software presentation provides a major opportunity to demonstrate its use as a practical decision-support tool for river conservation and management.