The yellow-billed cuckoo is a state-listed endangered bird in California. The largest population of cuckoos in California is on the meandering portion of the middle Sacramento River. I studied two time periods (1952 and 1987) of a 127-km study reach of the Sacramento River to document regeneration and spatial shifts in yellow-billed cuckoo habitat patches due to fluvial geomorphic processes, vegetation recruitment and succession over a 35-year period. The spatial co-occurrence of natural riparian vegetation and floodplain age <65 years were used to identify sub-patches of cottonwood forest, a preferred habitat element, within larger patches of contiguous riparian forest. Only 247 ha (15%) of the 1664 ha of habitat sub-patches identified in 1952 were coincident with those in 1987. Seventeen (27%) of the 62 sub-patches delineated for 1987 emerged anew and independently of the 1952 patches; the remaining 83% formed by shifting adjacent to the patches from 1952. Comparing observation data (1987–1990) with modelled patches (1987) indicates that 79% of the modelled sub-patches correctly predicted cuckoo presence or absence. The commission and omission errors were 7% and 14%, respectively. The goal of sustaining the yellow-billed cuckoo population will require that river channel management encourage channel meander dynamics and channel cut-off to maintain natural regeneration of cottonwood and willow pioneer plant communities. The active management of hydrodynamic (flow) and geomorphic processes, including the use of prescription flows and the removal of bank revetment (riprap), will be important tools towards achieving this goal. Copyright © 2012 John Wiley & Sons, Ltd.