River systems have been altered worldwide by dams and diversions, resulting in a broad array of environmental impacts. The use of a process-based, hierarchical framework for assessing environmental impacts of dams is explored here in terms of a case study of the Kootenai River, western North America. The goal of the case study is to isolate and quantify the relative effects of multiple dams and other river management activities within the study area and to inform potential restoration strategies. In our analysis, first-order impacts describe broad changes in hydrology (determined from local stream gages), second-order impacts quantify resultant changes in channel hydraulics and bed mobility (predicted from a 1D flow model), and third-order impacts describe consequences for recruitment of riparian trees (recruitment box analysis). The study area is a 233km reach bounded by two dams (Libby and Corra Linn). Different times of dam emplacement (1974 and 1938, respectively) allow separation of their relative impacts. Results show significant changes in 1) the timing, magnitude, frequency, duration and rate of change of flows, 2) the spatial and temporal patterns of daily stage fluctuation, unit stream power, shear stress, and bed mobility, and 3) the potential for cottonwood recruitment (Populus spp.). We find that Libby Dam is responsible for the majority of first and second-order impacts, but that both dams diminish cottonwood recruitment; operation of Corra Linn adversely affects recruitment in the lower portion of the study reach by increasing stage recession rates during the seedling establishment period, while operation of Libby Dam affects recruitment in the middle and upper portions of the study reach by changing the timing, magnitude, and duration of flow. We also find that recent experimental flow releases initiated in the 1990s to stimulate recovery of endangered native fish may have fortuitous positive effects on cottonwood recruitment potential in the lower portion of the river. This case study demonstrates how a process-based, hierarchical framework can be used for quantifying environmental impacts of dam operation over space and time, and provides an approach for evaluating alternative management strategies.