It is broadly recognized that flow regimes of urban streams are altered due to urban development and excess stormwater runoff. This consequently alters the stream hydraulic conditions which can have greater effect on the stream ecosystem structure and functioning particularly through channel disturbance, limiting refuge habitats. This study shows evidence of the effects of flow alteration due to urbanization on stream hydraulics by comparing the urban and natural reaches of the same stream. We characterize the degree and pattern of the hydraulic changes through 2D hydrodynamic modelling using ecologically relevant hydraulic metrics; Shields stress (τ*) that evaluates the channel disturbance based on bed material entrainment and habitat availability measured by the slackwater habitat (SWH) area. The results show that urban-induced flow alteration substantially alters the hydraulic changes. The frequency and magnitude of bed disturbance over the study period were predicted to be substantially greater in the urban stream than the natural stream. The urban stream showed the most unstable channel with the relative percent area of channel bed likely to be entrained as flow nears bankfull about 3x higher compared to the natural stream. The SWH area rapidly diminishes in the urban stream as discharge increases. These results demonstrate changes in stream hydraulic regimes due to urbanization that may impact on physical habitat in urban streams which may have extensive and significant impact on aquatic biota and ecosystems functions. The findings support a better mechanistic understanding of the link between urban-induced flow changes and degradation of stream physical habitat and thus help to inform of management protection actions.