AbstractCoupled simulations of surface and variably saturated subsurface flow, termed integrated hydrologic models (IHMs), can provide powerful insights into the complex dynamics of watersheds. The system of governing equations solved by an IHM is non‐linear, making them a significant computational burden and challenging to accurately parameterize. Consequently, a large fraction of the IHM studies to date have been “numerical hypothesis testing” studies, but, as parallel computing continues to improve, IHMs are approaching the point where they might also be useful as predictive tools. For this to become reality, the predictive uncertainty of such highly parameterized simulations must be considered. However, uncertainty is seldom considered in the IHM literature, likely due to the long runtimes of the complex simulations. The questions considered herein are how much uncertainty is there in an IHM for a common watershed simulation scenario, and how likely is it that any one realization of a system will give the same relative change as any other due to a perturbation in recharge? A stochastic ensemble of 250 permeability field realizations was used to show that uncertainty in a high‐mountain headwaters systems is dominated by the subsurface. Recharge perturbation scenarios echo these results, but the uncertainty of changes in streamflow or groundwater pressure heads were significantly smaller than the uncertainty in their base‐case values. The main finding is that IHMs do provide confident, predictive estimates of relative changes in watersheds, even when uncertainty in specific simulation outputs may be high.