Given the widespread presence of non-native vegetation in urban and Mediterranean watersheds, it is important to evaluate how these sensitive ecosystems will respond to activities to manage and restore native vegetation conditions. This research focuses on Del Cerro, a tributary of the San Diego River in California, where non-native vegetation dominates the riparian zone, creating flooding and fire hazards. Field data were collected in 2018 to 2021 and consisted of water depth, streamflow, and stream temperature. Our data set also captured baseline conditions in the floodplain before and after the removal of burned non-native vegetation in November 2020. Observed changes in hydrologic and geomorphic conditions were used to parameterize and calibrate a two-dimensional hydraulic model to simulate urban floodplain hydraulics after vegetation removal. We utilized the U.S. Army Corps of Engineers’ Hydrologic Engineering Center River Assessment System (HEC-RAS) model to simulate the influence of canopy loss and vegetation disturbance and to assess the impacts of vegetation removal on stream restoration. We simulated streamflow, water depth, and flood extent for two scenarios: (1) 2019; pre-restoration where non-native vegetation dominated the riparian area, and (2) 2021; post-restoration following the removal of non-native vegetation and canopy. Flooding after restoration in 2021 was more frequent compared to 2019. We also observed similar flood extents and peak streamflow for storm events that accumulated half the amount of precipitation as pre-restoration conditions. Our results provide insight into the responses of small urban stream reaches to the removal of invasive vegetation and canopy cover.