The North American beaver (Castor canadensis) is a managed species in the United States. In northern Wisconsin, as part of the state-wide beaver management program, the Chequamegon-Nicolet National Forest removes beavers from targeted trout streams on U.S. Forest Service lands. However, the success of this management program has not been evaluated. Targeted removals comprise only 3% of the annual beaver harvest, a level of effort that may not affect the beaver population. We used colony location data along Forest streams from 1987–2013 (Nicolet, northeast Wisconsin) and 1997–2013 (Chequamegon, northwest Wisconsin) to assess trends in beaver colony density on targeted trout streams compared to non-targeted streams. On the Chequamegon, colony density on non-targeted trout and non-trout streams did not change over time, while colony density on targeted trout streams declined and then stabilized. On the Nicolet, beaver colony density decreased on both non-targeted streams and targeted trout streams. However, colony density on targeted trout streams declined faster. The impact of targeted trapping was similar across the two sides of the Forest (60% reduction relative to non-targeted trout streams). Exploratory analyses of weather influences found that very dry conditions and severe winters were associated with transient reductions in beaver colony density on non-targeted streams on both sides of the Forest. Our findings may help land management agencies weigh more finely calibrated beaver control measures against continued large-scale removal programs.