Nitrogen and phosphorus emissions from urban sources degrade aquatic ecosystems. Reducing these emissions cost-effectively in an urban environment is challenging because they are non-point source pollutants and abatement strategies range from behaviour change for garden fertilizer use to large scale infrastructure investments. This paper analyses policy options for the Canning catchment in Western Australia with a dynamic and spatial hydro-economic model. Currently responsibility for N and P abatement is fragmented across government agencies. A coordinated cost-effective policy to meet N and P abatement targets in the case study catchment would cost A$0.5 billion over the next fifty years. The minimum cost is approximately doubled if the policy set excludes septic tank infill and constructed wetlands. Costs are significantly reduced if there is a city-wide policy to mandate the use of slow-release nitrogen fertilizer on public open space. We conclude that there is a significant benefit to society from adopting a coordinated approach to nitrogen and phosphorous abatement. Further, in this case study, a non-point source pollution problem can be addressed by abatement measures, such as infrastructure investment, that are directly observable.