Riparian habitat in the southwestern USA has undergone substantial degradation over the past century, prompting extensive management and restoration of these critical ecosystems. Most restoration efforts, however, do not account for life history traits or riverine complexity that may influence genetic diversity and structure. Here, we use simple sequence repeat (SSR) markers in four southwestern riparian species (Populus fremontii, Salix gooddingii, S. exigua, and Prosopis glandulosa) that occupy a geographically complex region to address four questions: 1) How is river connectivity related to genetic diversity and structure? 2) How do mating systems and dispersal mechanisms influence gene flow? 3) Is genetic diversity influenced by unidirectional water flow? 4) How do unregulated tributary and regulated river flows affect clonality and associated diversity? Our results identify five findings: 1) Patterns of genetic diversity and structure vary substantially across different species; 2) species with geographic distributions that include a large, perennial river exhibit the least genetic structure; 3) mating system, clonality, and seed dispersal are related to genetic structure; 4) genetic diversity is variable among species and populations, but does not increase or decrease unidirectionally; and 5) clonality and associated diversity does not differ along a regulated river relative to unregulated tributaries. Our multispecies approach to understanding how riverine complexity and life history traits influence genetic diversity and structure could be incorporated into management efforts to more closely match riparian species with their unique environments, thereby facilitating restoration success.