Natural disturbances play a fundamental role in maintaining habitat and landscape heterogeneity; however, these events can also have negative effects on some species. While we know that disturbances can reduce habitat quality for many species, leading to diminished populations and altered community structure, the effect of these events on individuals that continue to occupy affected areas remains unknown. We focused on understanding the impact of flood-mediated reduction of habitat quality on Swainson's Warblers (Limnothlypis swainsonii). In 2008, a catastrophic flood event occurred on the Mississippi River and its tributaries, severely affecting one of two locations where we had studied territorial males since 2004. To determine the impact of flooding on this species, we evaluated how body condition and apparent survival of males differed between locations and in pre-flood (2004-2007) and post-flood (2008-2010) periods. Body condition did not differ between locations after the flood, suggesting that flooding did not cause food limitation for this obligate ground forager. Apparent survival in the post-flood period was lower at both locations and led to near population extirpation at the heavily flood-impacted site. Overall, this study demonstrates the vulnerability of species to extreme hydrological events, an increasing threat due to climate change. Future research should focus on identifying species that are vulnerable to these events and determining appropriate conservation strategies. Conservation for the Swainson's Warbler should focus on identifying and conserving the highest elevation, least flood prone areas within bottomland hardwood forests and managing those areas for thick understory vegetation.