We studied discharge data from stream gauges located in natural and anthropogenically modified river basins of the Northern Rocky Mountains over 59 years. We applied linear and nonlinear models to the data to determine what, if any, alterations have occurred in the annual flow regimes. By comparing the different results from the natural and anthropogenically modified river basins, we were able to distinguish the impacts that climate change and anthropogenic modifications have had on flow regimes in the Northern Rocky Mountains over the period of record. We found that regional climate change has not significantly altered the natural flow regimes. However, we did find an underlying cyclical pattern in the total amount of annual discharge in both the natural and anthropogenically modified river basins. This suggests a strong link between the quantity of runoff and some kind of hydroclimatologic cycle. Conversely, direct basin anthropogenic modifications such as damming, irrigation, and urbanization have caused a decrease in the difference between the minimum and maximum annual discharges and a decrease in the daily variations of flows across the Northern Rocky Mountains. In general, direct anthropogenic modifications of the river basins have altered the flow regimes to a much greater extent than climate change.