We evaluated the relationship between natural vegetative disturbance and changes in stream habitat and macroinvertebrate metrics within 33 randomly selected minimally managed watersheds in central Idaho and western Montana. Changes in stream reach conditions were related to vegetative disturbance for the time periods from 1985 to 1993 and 1993 to 2000, respectively, at the following three spatial scales; within the stream buffer and less than 1 km from the evaluated reach, within the watershed and within 1 km of the stream reach, and within the watershed. Data for stream reaches were based on field surveys and vegetative disturbance was generated for the watershed above the sampled reach using remotely sensed data and geographical information systems. Large scale (>100 ha) vegetative disturbance was common within the study area. Even though natural vegetative disturbance rates were high, we found that few of the measured attributes were related to the magnitude of vegetative disturbance. The three physical habitat attributes that changed significantly were sinuosity, median particle size, and percentage of undercut bank; each was related to the disturbance in the earlier (1985–1993) time frame. There was a significant relationship between changes in two macroinvertebrate metrics, abundance and percent collectors/filterers, and the magnitude of disturbance during the more recent time period (1993–2000). We did not find a consistent relationship between the location of the disturbance within the watershed and changes in stream conditions. Our findings suggest that natural vegetative disturbance within the northern Rocky Mountains is complex but likely does not result in substantial short-term changes in the characteristics of most stream reaches.