<p>Half of the world’s population currently lives in cities, leading to significant landscape transformations that affect freshwater ecosystems. These changes include increased imperviousness and water runoff, frequent municipal and industrial discharges, and the destruction of riparian corridors and floodplains, resulting in a consistent decline in biodiversity and ecosystem services, and posing new challenges for both environmental and human health. In the last decades, we observed an increase in water-related policies, echoing growing concern with water safety and freshwater ecosystems degradation. However, existing policies frequently fail to provide practical or efficient results or are insufficient. The present manuscript aims to highlight relevant international legislation and directives and to identify potential gaps that should be tackled to promote the protection of urban river and stream ecosystems as well as human health in cities. Despite the existence of EU norms that can protect the urban river and streams ecosystems in the European Union, such as the Water Framework Directive, the Habitats Directive, the Environmental Liability Directive and the Nature Restoration Regulation, or different agendas at a global level, the legislation is dispersed, subject to different interpretations and to conflicting interests in the city’s management. Therefore, urban freshwater ecosystems would benefit from the establishment of specific legislation that supports the action of municipal authorities, protecting their biodiversity and safeguarding adequate ecosystem functioning, the existence of floodplains, natural margins, and riparian forests, to guarantee a safe environment and improved well-being for the population of cities.</p>