In bifurcating rivers, an intervention aimed at flood risk reduction may trigger a change in discharge distribution and thus influence water levels throughout the entire river system. This article aims at assessing the impact of interventions on system-wide water levels, explicitly accounting for a range of discharges and model parameter uncertainty. An idealized 1D model with dimensions of the bifurcating Dutch Rhine River is used. The results show that an unwanted increase in water levels downstream of the intervention occurs due to an increased discharge if a single intervention is implemented in a distributary. This effect can be counteracted by implementing a second intervention that balances the hydraulic effect of the first intervention at the bifurcation. However, unwanted water level increases still occur at other discharges. Furthermore, while interventions may reduce local water-level-uncertainty, it appears that uncertainty in discharge distribution is not reduced. This implies that flooding probabilities cannot be reduced throughout the entire river system by the implementation of interventions in upstream reaches. Concluding, for intervention design in a bifurcating river, it is important to consider the entire river system and explicitly account for a range of discharge conditions to avoid unwanted water level increases throughout the river system.