Rivers and streams form a longitudinal network in which physical conditions and biological processes change through the river system. Geomorphology, topography, geology and hydraulic conditions change from site to site within the river system, thereby creating a complex network of reaches that are dominated by a hierarchy of physical processes. The complexity is further enhanced by local human alteration of the physical structure, natural processes and alteration of the riparian areas. The aim of the study was to analyse variations in land use and riparian characteristics along small Danish streams and to determine the effect of channelisation on physical habitats. Physical stream characteristics were measured in 149 stream small and medium sized Danish streams (catchment area: 0.1 to 67.2 km2). The measured physical parameters included discharge, stream slope, width, depth, current velocity, substrata and coverage of macrophytes. Riparian land use, valley form and information on channelisation and channel dredging were also collected. Small headwater streams were either dominated by forests or semi-natural land use. In contrast, the riparian areas of the streams in the larger streams were dominated by agricultural or semi-natural / meadow land use. The results suggest that a combination of within-system variations in geomorphological, hydrological and geological conditions as well as human alterations of the natural environment in small Danish catchments facilitate discontinuous changes to the stream bed substrata and in-stream habitats. The physical habitats and substratum characteristics of the channelised streams were significantly different from the structure in natural streams unaffected by physical modifications. Riparian land use and valley form potentially influence the degree of channelisation, i.e. a confined and steep valley (V-shaped) is less likely to be used for agricultural production compared to a broad valley. The results are useful to water managers, who seek to identify natural and impacted physical conditions in large river systems.