The effects of Hurricane Katrina on benthic fauna and habitat quality in coastal waters of Louisiana, Mississippi, and Alabama, USA, were assessed in October, 2005, 2 months after the hurricane made landfall between New Orleans, LA and Biloxi, MS. Benthic macrofaunal samples, sediment chemical concentrations, and water quality measurements from 60 sites in Lake Pontchartrain and Mississippi Sound were compared with pre-hurricane conditions from 2000–2004. Post-hurricane benthic communities had significant reductions in numbers of taxa, H′ diversity, and abundance as well as shifts in composition and ranking of dominant taxa. These effects were not associated with changes in chemical contamination, organic enrichment of sediments, or hypoxia and were likely due to hurricane-related scouring and changes in salinity.