1. System Aqua has been designed to meet the growing need for an objective, reproducible and comprehensive tool for assessing the conservation value of lakes and watercourses in Sweden. The system may be used to provide an integrated assessment of whole catchments as well as their component waters. Emphasis is placed on biological qualities, with biodiversity as a focal concept. 2. Biodiversity is evaluated by five criteria characterized by indicators, varying in number from three to five. The criteria are structural diversity, naturalness, rarity, species richness and representativeness, and the biotic groups evaluated consist of riparian vegetation, macrophytes, algae, macroinvertebrates, fish and nesting birds. 3. Indicators are scored from 0 to 5, where 5 reflects the highest biodiversity or the highest natural value, and 0 an extremely uniform or highly impacted habitat. 4. A numerical index value, based on weighted scores of assessed indicators, is obtained for each criterion. The indices are presented in an easily understandable criteria profile, where the proportion of indicators used reflects the confidence of the assessment.