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While for most of a landscape, urbanization leads to a significant habitat loss, rivers in urban areas are usually maintained or developed for their drainage function. Rivers are often the most important biophysical and ecological connection of cities with their surrounding ecosystems, although usually heavily altered due to urban impacts. For the conservation of urban rivers as ecological corridors, it is important to assess the impact of typical urban threats on habitat quality. In this study, we used the InVEST (Integrated Valuation of Environmental Services and Trade-offs) habitat quality model to assess the individual and combined impacts of built-up areas, first- and second-order road and water pollution from urban drainage, and wastewater discharge on habitat quality within a 200 m wide river corridor. The Pochote River in León, Nicaragua, was used as a case study. Our results show the spatial distribution and magnitude of the individual threat impacts, as well as the respective contribution of each threat to the overall impact of urbanization on the habitat quality within the river corridor. While close to the city center, all threats almost equally contributed to severe habitat degradation, while further downstream, an individual threat influence became more distinct with only water pollution having a consistent negative impact. We concluded that the InVEST habitat quality model can be used to assess the impact of typical urban threats on habitat quality in river corridors at a high spatial resolution. The results can help to improve urban planning and development to improve habitat conservation along urban rivers.