We assess changes in runoff timing over the last 55 years at 21 gages unaffected by human influences, in the headwaters of the Columbia-Missouri Rivers. Linear regression models and tests for significance that control for “false discoveries” of many tests, combined with a conceptual runoff response model, were used to examine the detailed structure of spring runoff timing. We conclude that only about one third of the gages exhibit significant trends with time but over half of the gages tested show significant relationships with discharge. Therefore, runoff timing is more significantly correlated with annual discharge than with time. This result differs from previous studies of runoff in the western USA that equate linear time trends to a response to global warming. Our results imply that predicting future snowmelt runoff in the northern Rockies will require linking climate mechanisms controlling precipitation, rather than projecting response to simple linear increases in temperature.