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.