Ecosystem approaches to management require monitoring of processes and species indicative of the integrity of the system in order to understand the effects of management and other perturbations. We examined the effects of three timber harvest options (single-tree selection, patch cuts, no harvest) on the reproductive biology of a possible indicator of bottomland forest ecosystem integrity, the prothonotary warbler (Protonotaria citrea). Timber harvests reduced the number of available nest cavities, reduced the density of breeding males on the plots, and increased the sizes of male territories. However, timber harvest had no obvious effect on nest predation or brood parasitism frequencies. Brood parasitism was instead related to distance from a nearby levee, a main source of brown-headed cowbirds (Molothrus ater) in the area. Productivity remained similar within suitable habitat regardless of treatment. Reproductive success was strongly influenced by annual variation, which we attribute to the timing and extent of annual flooding, a fundamental ecosystem process in floodplain forests. Continued anthropogenic alterations in flooding patterns may have a greater influence than current timber management on the future population levels of prothonotary warblers in the Mississippi Alluvial Valley. This species, with others, could play a valuable role in an ecosystem-oriented monitoring program.