In 1995, mapping and classification of riparian vegetation along the Mojave River in southern California revealed an 8-km reach in which riparian cottonwoods (Populus fremontii Wats.) were stressed or dying. We tested a set of predictions based on the inference that cottonwood decline was an indirect result of lowered water-table levels following flood-related channel incision. Comparisons of topographic cross-sections from 1963 and 1997, indicated a net change in channel elevation between −0·71 and −3·6 m within zones of cottonwood stress and mortality. Ages of young cottonwood and willow stems adjacent to the present channel and radial stem growth of surviving cottonwoods were consistent with the inference that channel incision, associated with sustained flooding in January and February of 1993, lowered channel elevations throughout the affected reach. Well records and soil redoximorphic features indicate that channel incision caused net water-table declines ⩾1·5 m on portions of the adjacent flood plain where cottonwood stand mortality ranged between 58 and 93%. In areas where water-table declines were estimated to be <1·0 m, stand mortality was 7–13%.