A major challenge in assessing the hydrologic effect of climate change remains the estimation of uncertainties associated with different sources, such as the global climate models, emission scenarios, downscaling methods, and hydrologic models. There is a demand for an efficient and easy-to-use rainfall–runoff modeling tool that can capture the different sources of uncertainties to generate future flow simulations that can be used for decision making. To manage the large range of uncertainties in the climate change impact study on water resources, a neural network–based rainfall–runoff model—namely, Bayesian neural network (BNN)—is proposed. The BNN model is used with Canadian Centre for Climate Modelling and Analysis Coupled GCM, versions 1 and 2 (CGCM1 and CGCM2, respectively) with two emission scenarios, Intergovernmental Panel on Climate Change (IPCC) IS92a and Special Report on Emissions Scenarios (SRES) B2. One widely used statistical downscaling model (SDSM) is used in the analysis. The study is undertaken to simulate daily river flow and daily reservoir inflow in the Serpent and the Chute-du-Diable watersheds, respectively, in northeastern Canada. It is found that the uncertainty bands of the mean ensemble flow (i.e., flow simulated using the mean of the ensemble members of downscaled meteorological variables) is able to mostly encompass all other flows simulated with various individual downscaled meteorological ensemble members whichever CGCM or emission scenario is used. In addition, the uncertainty bands are also able to typically encompass most of the flows simulated with another rainfall–runoff model, namely, Hydrologiska Byråns Vattenbalansavdelning (HBV). The study results suggest that the BNN model could be used as an effective hydrological modeling tool in assessing the hydrologic effect of climate change with uncertainty estimates in the form of confidence intervals. It could be a good alternative method where resources are not available to implement the general multimodel ensembles approach. The BNN approach makes the climate change impact study on water resources with uncertainty estimate relatively simple, cost effective, and time efficient.