The erosion of mountain belts controls their topographic and structural evolution and is the main source of sediment delivered to the oceans. Mountain erosion rates have been estimated from current relief and precipitation, but a more complete evaluation of the controls on erosion rates requires detailed measurements across a range of timescales. Here we report erosion rates in the Taiwan mountains estimated from modern river sediment loads, Holocene river incision and thermochronometry on a million-year scale. Estimated erosion rates within the actively deforming mountains are high (3-6 mm yr(-1)) on all timescales, but the pattern of erosion has changed over time in response to the migration of localized tectonic deformation. Modern, decadal-scale erosion rates correlate with historical seismicity and storm-driven runoff variability. The highest erosion rates are found where rapid deformation, high storm frequency and weak substrates coincide, despite low topographic relief.