Aims The Wami River system is among the most important rivers for riparian plant biodiversity conservation but it is potentially threatened by anthropogenic activities. This study was aimed to determine riparian plant species diversity and distribution patterns in relation to the anthropogenic disturbances. Methods The transect method was used to collect vegetation data. Transects were established perpendicular to the river at intervals of 50 m downstream and five plots were systematically established, separated by 5-m distance along each transect. Results A total of 261 plant species in 68 families were recorded in the Wami River system with a Shannon diversity index in the range of 1.63 to 2.94 and a significantly decreasing trend downstream. Using the Two Way Indicator Species Analysis (TWINSPAN), three plant communities (A, B and C) emerged based on variations in riparian plant species composition among sites. Canonical correspondence analysis (CCA) indicated that the spatial pattern of riparian plant species was significantly influenced by environmental variables. This implies that the plant species composition gradients and spatial assemblages of vegetation communities are a result of human disturbances. Because of the fragile nature of the riparian system, some species are more vulnerable than others and hence there is an urgent need for better land use planning to conserve riparian plant biodiversity in the sub-Basin of Wami River.