Flooding in semi-arid streams is highly variable but distinguished from its humid counterpart in terms of forcing conditions, landscape response, flood severity, and stream-aquifer connectivity. These floods have the potential for great benefit in a water-limited environment, but also great devastation when powerful floods encounter human infrastructure. This dissertation employs an integrative approach to address several facets of flooding in semi-arid streams. In particular, information from field sampling during flood events combined with modeling are used to evaluate the processes of post-disturbance sediment transport, flood routing, transient bank storage, and stream disconnection. The major findings show: (1) Suspended sediment composition in floods following wildfire depends on the number, timing, and intensity of preceding storms and flood events, implicating overland flow hillslope processes as a dominant mass wasting mechanism (2) Isotopic chemographs for two representative intense convective storm events demonstrate that the flash flood bore develops from predominantly high elevation event water that overcomes, incorporates, and pushes baseflow to the front of the hydrograph peak (3) Isotope information combined with a plug-flow model can simulate this flood bore mixing process simultaneously in two separate canyons in the basin in order to calculate the timing and quantity of flow; this could be a useful tool for watersheds that are not extensively instrumented, or for calibrating a more complex or distributed model, (4) For a stream connected to an underlying aquifer, a circulation pattern develops at the onset of flooding that causes an upwelling of antecedent water into the unsaturated zone, challenging the assumptions of one dimensional, lateral flow and transport into the streambank, and (5) For small stream-aquifer disconnections, large increases in infiltration, large decreases in seepage, and a dominantly vertical profile for floodwater were observed. This implies that a stream that supports a wide riparian corridor may be in danger of vegetation die-offs with even shallow depletions of the groundwater table.