Forest harvesting directly affects headwater systems, causing changes in catchment hydrology and riparian habitats. We investigated geomorphological impacts of clearcut harvesting on headwater systems and their recovery in the boreal mixedwood forests of northwestern Ontario, Canada. We studied 30 headwater streams (width <3 m), 24 in previously clearcut sites and six in undisturbed mature forests as reference. Each sampled stream had two segments, i) in clearcut 10 m away from the cut edge and ii) in riparian buffer of the larger stream to which it flows. Using MANOVA and discriminant function analysis, we examined harvesting impacts on stream width, depth, number of stream channels, riparian width, ground exposure, canopy exposure and organic matter depths as disturbance index in clearcut chronosequence and reference forest. Among all these factors we found canopy exposure contributed most to the observed harvesting impacts, which remained significantly high up to 15 years after clearcutting compared to the reference forest. Stream width and number of stream channels were also significantly high in clearcut sites for up to three years after harvesting but the differences tapered within 10 years. Streams were shallower in recently harvested sites, a difference that remained detectable even 23 years after clearcutting. General impacts of harvesting adjacent to headwater streams and their riparian zones were detectable at least until 15 years after harvesting. Although it is likely that harvest related biophysical damage in the headwater systems have negative effects on the aquatic ecosystems of the larger streams no study in the boreal forests has yet evaluated this direct link. We argue that although protecting all small streams and their headwater system by buffers is not possible, biophysical damage during harvesting can be avoided by complying with guidelines that forbid harvesting equipments near waters edge and retaining residual vegetation along small streams.