The widespread degradation of riparian ecosystems requires that we more fully understand patterns of plant diversity at multiple scales to inform restoration and conservation efforts locally and regionally. We analyzed the distribution of riparian plant diversity in California's Sacramento - San Joaquin Valley, focusing on patterns found at three spatial scales, to support present and future large river habitat restoration initiatives. We examined species richness and complementarity between sample units at the riverscape, inter-riverine, and intra-riverine scales. At the coarsest riverscape scale, spatial patterns of native riparian richness were driven by herbaceous species, while woody species were largely cosmopolitan. Riverscape riparian species richness centered over the California Bay-Delta region, forming a natural geographic ecotone between the two largest watersheds. Inter-riverine richness and turnover between six watershed study locations also indicated native riparian flora shifts mid-valley. Fine-scale, intra-riverine riparian floras from the Sacramento and Cosumnes River floodplains had spatial patterns among sites that relate to successional sequences. These fine-scale patterns suggest flood-induced disturbance is an important factor in promoting heterogeneous habitats and herbaceous species turnover. Our results are consistent with modern riverscape ecological theory; wherein natural disturbances initiate patterned structural diversity that in turn promote aquatic and terrestrial biodiversity. If biodiversity is to be a goal of future ecosystem restoration efforts, these findings suggest that hydrological processes promoting diversity and distribution of native riparian herbaceous flora need more attention. Furthermore, to be effective, large ecosystem restoration efforts require multi-scale approaches to assess baseline patterns of distribution and to develop appropriate benchmarks.