Braided river systems are an important source for groundwater recharge, but their complex morphology makes river–groundwater exchange fluxes difficult to estimate. Their river channel morphology changes frequently after floods, which has effects on recharge rates that have rarely been studied in the past. This work aims to isolate the effects of changes in braided river morphology on groundwater recharge for two sections of the Wairau River and Waikirikiri River in New Zealand. For each study site, two different river morphology variants of a fully coupled surface water–groundwater model utilizing high-resolution DEMs of river bathymetry before and after a major flood event were set up while keeping parameterization and boundary conditions the same. The models demonstrate that flood-induced morphology changes in braided river systems alter groundwater recharge. We identify features, both simulated and observed, that explain the direction of change. Features that increase groundwater recharge are a larger braidplain aquifer extent and volume, larger wetted area and, specifically, an increase of areas with high exchange rates in locations of larger gradients between braidplain aquifer and regional aquifer. These factors influence groundwater recharge independent of connection (Wairau River) or disconnection (Waikirikiri River) of the system to the regional aquifer, albeit with different magnitudes. An extension of our research to other braided rivers is needed to more broadly generalize our findings.