Although hurricanes have been implicated in causing shifts in waterbird use of individual colonies, little is known about whether or not these effects are consistent across broader areas affected by a storm. We examined the effects of Hurricane Rita, and to a lesser extent Katrina, and a subsequent drought, on the nesting activity of waterbirds across colonies located in southern Louisiana. Using ground counts, we compared changes in numbers of nesting pairs between 2005 and 2006, the years encompassing the hurricanes and drought, with changes between 2004 and 2005. Following the hurricanes, colonies were more likely to become inactive or experience large shifts in numbers of nesting pairs, compared with the period before the hurricanes. Although one third of the surveyed colonies became inactive following the hurricanes, total numbers of nesting birds of most species increased. We hypothesize that these increases were the result of birds shifting from damaged to active colonies. Colony use was negatively associated with the maximum wind speeds experienced at each site, apparently as a result of damage to nesting habitat. There were no associations of colony use with either storm-related flooding or localized rainfall during the drought; however, this may be due to manipulation of water levels by management agencies. Our results suggest that monitoring colonies over a broad area is necessary to understand the influence of hurricanes on the nesting activity of waterbirds.