Vegetation and riverine structures were compared among urban and several semi-natural rivers by applying direct gradient analysis and ordination method. Urban rivers showed different species composition from the semi-natural ones. Species composition of semi-natural rivers depended on the geographical positions, such as the upstream, midstream, and downstream and on micro-topographies, such as the waterside, flooding bed, and embankment. Semi-natural rivers showed gentle change in micro-topography, whereas urban one did not so. Our restoration plan to improve the ecological quality of the degraded urban river by imitating semi-natural river was prepared based on those data.