Hyporheic zones (HZs) influence biogeochemistry at the local reach scale with potential implication for water quality at the large catchment scale. The characteristics of the HZs (e.g., area, flux rates, and residence times) change in response to channel and aquifer physical properties, as well as to transient perturbations in the stream–aquifer system such as floods and groundwater withdraws due to evapotranspiration (ET) and pumping. In this study, we use a numerical model to evaluate the effects of transient near-stream evapotranspiration (ET) on the area, exchange flux, and residence time (RT) of sinuosity-induced HZs modulated by regional groundwater flow (RGF). We found that the ET fluxes (up to 80 mm/day) consistently increased HZ area and exchange flux, and only increased RTs when the intensity of regional groundwater flow was low. Relative to simulations without ET, scenarios with active ET had more than double HZ area and exchange flux and about 20% longer residence times (as measured by the median of the residence time distribution). Our model simulations show that the drawdown induced by riparian ET increases the net flux of water from the stream to the nearby aquifer, consistent with field observations. The results also suggest that, along with ET intensity, the magnitude of the HZ response is influenced by the modulating effect of both gaining and losing RGF and the sensitivity of the aquifer to daily cycles of ET withdrawal. This work highlights the importance of representing near-stream ET when modeling sinuosity-induced hyporheic zones, as well as the importance of including riparian vegetation in efforts to restore the ecosystem functions of streams.