Abstract: Naturally induced longitudinal disconnectivity in the form of channel-spanning logjams creates backwaters along headwater streams that reduce velocity and transport capacity, create at least temporary storage sites for finer sediment and organic matter, and enhance biological processing and uptake of nutrients. Land uses that reduce wood recruitment and instream storage result in reduced stream complexity and increased longitudinal connectivity in headwater rivers. We examine three scales of naturally occurring longitudinal disconnectivity in headwater streams of the Colorado Front Range and the implications for channel process and form of historical alterations in disconnectivity. Basin-scale disconnectivity at channel lengths of 102–103 m results from downstream alternations between steep, narrowly confined valley segments with single-thread channels, and lower gradient, wider, valley segments with multi-thread channels. This variation in valley geometry likely reflects differences in average spacing between joints in bedrock outcrops, which influences bedrock weathering and erosion. Greater volumes of wood stored in the wide valley segments correlate with more closely spaced channel-spanning logjams and greater storage of fine sediments and organic matter. Reach-scale disconnectivity at channel lengths of 101–102 m results from the presence of numerous, closely spaced channel-spanning logjams, which cumulatively store substantial amounts of fine sediment and organic matter. The backwater effects associated with an individual jam can result in the accumulation of up to ~11m3 of fine sediment upstream from the jam, of which as much as 21% is organic matter. Unit-scale disconnectivity at channel lengths of 100–101 m results from the presence of an individual channel-spanning logjam, which locally alters bed gradient, substrate composition, bedform dimensions, and the transport of sediment and organic matter. The transport and storage of instream wood is a critical component of disconnectivity at all spatial scales examined. Land uses such as timber harvest, flow regulation, and placer mining that result in reduced wood recruitment or removal of instream wood appear to create an alternative stable state in which channels are unable to retain wood because of reduced debris roughness. The net effect of reduced longitudinal disconnectivity is increased transport of fine sediment and organic matter and reduced biological uptake of nutrients. The altered headwater streams become leaky with respect to fine sediments and nutrients. [Copyright &y& Elsevier]