Large-scale disturbances, by affecting habitat suitability, can influence bird populations and communities. Although we know that disturbances can lead to population decreases and shifts in community structure, our understanding of finer-scaled mechanisms leading to these patterns is limited. We focused on why some territories remain occupied by a species following a large-scale disturbance, while others are abandoned. The Swainson's Warbler (Limnothlypis swainsonii) is especially susceptible to flooding because of its preference for nesting in thick understory vegetation and foraging in leaf litter. In 2008, a major flood inundated a study site where we have studied Swainson's Warblers since 2004. In 2008 and 2009, we resurveyed 42 Swainson's Warbler territories that were occupied between 2005 and 2007 and examined changes in habitat structure and composition and prey abundance influencing territory abandonment. Occupancy declined between the preflood and postflood surveys. Territory abandonment was associated with decreases in leaf litter cover, increases in cover of green vegetation, and decreases in density of total understory stems and giant cane (Arundinaria gigantea) between the preflood and flood periods. Despite the partial recovery of habitat structure and prey abundance after the flood, Swainson's Warbler occupancy did not recover in subsequent years. Multiple habitat variables, including leaflitter cover, density of woody stems, understory density, and prey abundance have been identified as important for Swainson's Warblers, and these results suggest that leaf litter may be especially important in influencing habitat-selection decisions following flood disturbance.