Despite their limited area relative to the global ocean, coastal zones—the regions where land meets the sea—play a disproportionately important role in generating ecosystem services. However, coastal ecosystems are under increasing pressure from human populations. In particular, urban stormwater is an increasingly important threat to the integrity of coastal systems. Urban catchments exhibit altered flow regimes that impact ecosystem processes and coastal foodwebs. In addition, urban stormwater contains complex and unpredictable mixtures of chemicals that result in a multitude of lethal and sublethal impacts on species in coastal systems. Along the western coast of the United States, we estimate that hundreds of billions of kilograms of suspended solids flow off land surfaces and enter the Northern California Current each year. However, 70% of this pollution could be addressed by treating only 1.35% of the land area. Determining how to prioritize treatment of stormwater in this region requires a clear articulation of objectives—spatial distribution of appropriate management actions is dependent on the life histories of species, and management schemes optimized for one species may not achieve desired objectives for other species. In particular, we highlight that the scale of stormwater interventions must match the ecological scale relevant to species targeted by management. In many cases, management and policy will require mechanisms in order to ensure that local actions scale-up to efficiently and effectively achieve management objectives. In the face of rapid urbanization of coastal zones, failure to consider the match of management and ecological scales will result in the continued decline of coastal ecosystems and the species they support. This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.