Worldwide countries face challenges to restore and preserve water resources. This paper analyses how governance approaches support the attainment of water quality ambitions set out in the European Water Framework Directive and the UN Sustainable Development Goals. To this end, the connection between the physical water system and the governing legal and societal systems is explored, using scientific literature and empirical material on governance approaches in the subdomains of drinking water resources, freshwater ecosystems and bathing water in The Netherlands. The results show the effects of the intricate relationship between water system characteristics and the drivers of water quality versus the various elements of a governance approach. For instance, hydrological, morphological and chemical objectives set different demands on governance conditions, related to the scale, roles and responsibilities of actors who need to be involved and coherence of the legal and policy frameworks in place. These demands can also be different during the different stages of a policy process. Choices made in a governance approach (who to involve, availability and use of legal instruments, measures and monitoring) may therefore influence the level of water quality improvement that can be achieved. A joint approach from the social-economic, legal and ecological knowledge domain during all stages of a policy process is necessary to overcome such unintended results.