The braided rivers and floodplains in the Upper Waitaki Basin (UWB) of the South Island of New Zealand are critical habitats for endangered and threatened fauna such as the black stilt. However, this habitat has degraded due to introduced predators, hydropower operations, and invasive weeds including Russell lupins. While conservation efforts have been made to restore these habitats, flood events may provide a natural mechanism for removal of invasive vegetation and re-creation of natural floodplain habitats. However, little is understood about the hydraulic effects of floods on vegetation and potential mortality in these dynamic systems. Therefore, this thesis analyzed the flood-induced processes that cause lupin mortality in a reach of the Ahuriri River in the UWB, and simulated various sized flood events to assess how and where these processes occurred. To determine the processes that cause lupin mortality, post-flood observations were utilized to develop the hypothesis that flood-induced drag, erosion, sediment deposition, inundation, and trauma were responsible. Field and laboratory experiments were conducted to evaluate and quantify these individual processes, and results showed that drag, erosion, sediment deposition and inundation could cause lupin mortality. Utilizing these mortality processes, mortality thresholds of velocity, water depth, inundation duration, and morphologic changes were estimated through data analysis and evaluation of various empirical relationships. Delft3D was the numerical model used to simulate 2-dimensional flood hydraulics in the study-reach and was calibrated in three stages for hydraulics, vegetation, and morphology. Hydraulic calibration was achieved using the study-reach topography captured by Structure-from-Motion (SfM) and various hydraulic data (depth, velocity, and water extent from aerial photographs). Vegetation inclusion in Delft3D was possible utilizing a function called ‘trachytopes’, which represented vegetation roughness and flow resistance and was calibrated utilizing data from a lupin-altered flow conveyance experiment. Morphologic calibration was achieved by simulating an observed near-mean annual flood event (209 m3 s-1) and adjusting the model parameters until the simulated morphologic changes best represented the observed morphologic changes captured by pre- and post-flood SfM digital elevation models. Calibration results showed that hydraulics were well represented, vegetation inclusion often improved the simulated water inundation extent accuracy at high flows, but that local erosion and sediment deposition were difficult to replicate. Simulation of morphological change was expected to be limited due to simplistic bank erosion prediction methods. Nevertheless, the model was considered adequate since simulated total bank erosion was comparable to that observed and realistic river characteristics (riffles, pools, and channel width) were produced. Flood events ranging from the 2- to 500-year flood were simulated with the calibrated model, and lupin mortality was estimated using simulation results with the lupin mortality thresholds. Results showed that various degrees of lupin mortality occurred for the different flood events, but that the dominant mortality processes fluctuated between erosion, drag, and inundation. Sediment deposition-induced mortality was minimal, but was likely under-represented in the modeling due to poor model sediment deposition replication and possibly over-restrictive deposition mortality thresholds. The research presented in this thesis provided greater understanding of how natural flood events restore and preserve the floodplain habitats of the UWB and can be used to aid current and future braided river conservation and restoration efforts.