We present case studies supporting management of two rare plant species in tidal wetlands of the San Francisco Estuary. We used empirical demographic analyses to identify factors to enhance population establishment and survival of Chloropyron molle subsp. molle (Orobancaceae), an annual hemiparasite, and to compare reintroduced with natural populations. Twelve years after outplanting, the reintroduced population persists but is in decline; impediments to success include the lack of adaptive management response to weed invasions and muted variance in hydrology. Transplantation of Lilaeopsis masonii (Apiaceae), a rhizomatous perennial herb, failed to meet success criteria for mitigation at local project scale, but dispersal and establishment of metapopulation patches indicated persistence at the landscape scale. This species has been found to be genetically indistinct from a widespread congener, and has few threats to persistence so long as suitable habitat is present. These two examples demonstrate the need for integrated conservation management strategies that prioritize habitat connectivity and maintain physical processes to support dispersal in response to sea level rise. For the hemiparasite, assisted colonization may sustain populations threatened by sea level rise, but only if a strong commitment to effective stewardship is realized.