Tropical forest vegetation occurs within a narrow corridor along the semi-arid lower floodplain of the Tana River, Kenya. An inventory of the woody flora and ecological study of 12 forest areas in the Tana River National Primate Reserve (TRNPR) describe the composition and structure of this riverine forest ecosystem and identify patterns of regional and local diversity. Only 175 species in 49 families are recorded in the woody flora, but the geographic affinities of 98 species are from four major floristic regions in Africa: Zanzibar-Inhambane (31%), Somalia-Masai (16%), Guinea-Congolian (12%), and Zambezian (1%). Ten species are rare and/or disjunct. Forests have a disturbed physiognomy characterized by a low mean height (14.4 m), high species importance attributable to a few trees, low density (409 ha−1) and coverage (23.1 m2 ha−1) of trees > 10 cm dbh, and an abundance of palms and lianes. Changes along the river in sediment deposition and hydrology explain the high diversity of landforms and corresponding forest types in the TRNPR vicinity, but the absence of trees which are most important near Bura, Acacia elalior, and near Wema, Barringtonia racemosa, suggests that the regional diversity of the ecosystem is inadequately protected. Preservation of key resources, such as the endangered primates, should be coupled with protection of the forest heterogeneity that characterizes this dynamic landscape.