Conservation frequently requires the preservation or restoration of ecosystems in human-altered landscapes. Understanding these ecosystems requires matching patterns with processes at appropriate scales. On floodplains this necessitates coupling plant distributions with fine- and broad-scale hydrologic patterns. This is particularly important when target species are of conservation concern, such as the blue elderberry (Sambucus mexicana). Blue elderberry is the sole host plant for the federally threatened Valley elderberry longhorn beetle, yet controls on the shrub's distribution have largely been untested. We used nested hierarchical analyses to test hypotheses about the role of broad- and fine-scale variables structuring the distribution of elderberry in one undammed and three dammed rivers in California's Central Valley (USA). Elderberry presence across the floodplains was primarily driven by broad-scale hydrologic regime, as represented by the relative elevation, floodplain width, and lateral distance of shrubs from the stream, and secondarily by sediment texture and topography. The patchy spatial distributions of elderberry were similar among the rivers, but habitat quality characteristics (i.e., controls on abundance and size) were driven by divergent variables with high stochasticity. We can improve our understanding of species distributions and outcomes of recovery efforts by scaling floodplain conservation efforts to broad-scale hydrologic patterns and by detecting crucial variables using a multi-scale methodology. Within these relatively large, self-defined landscape units, certain precautions and the application of an adaptive management approach could be employed to address the local-scale uncertainty in large-scale conservation efforts.