The Great Lakes are an important source of fresh water, recreation resource and transportation corridor for the Midwestern United States and Canada. The timing and quantity of fresh water inputs and how those may change under projections of future climate change are important for understanding how conditions, including river flows, and lake levels, within the region may be affected. Water quality and the density and diversity of in-stream habitats are responsive to changes in the distribution of daily streamflow, something not typically included in studies of climate change impacts. Projections of precipitation and air temperature changes in the four states surrounding Lake Michigan from the IPCC AR4 were downscaled and biascorrected before being used to drive a large-scale hydrology model and produce maps of surface runoff and baseflow. These were then routed along drainage networks for regional rivers, and hydrologic metrics describing aspects of the distribution of daily flows important for hydrology and in-stream ecology were computed. The impact of regional climate change projections on early- (water years 2010–2039) and midcentury (water years 2040–2069) streamflow was highly variable; however, by the late-century period (water years 2070–2099) annual streamflow was found to have increased in all rivers. Seasonally, winter and spring flows increased significantly by the late-century period, but summer flows become more variable with a decrease in low-flows and an increase in peak-flows. The number of days with flows above the annual mean-flow (T_Qmean) decreased in summer, but flashiness (R-B Index) increased.