In recent decades, there has been increasing interest in the application of ecological indices to assess ecosystem condition in response to anthropogenic activities. DeLuca et al. (2008) developed an Index of Waterbird Community Integrity (IWCI) to evaluate breeding waterbird response to anthropogenic activities in the Chesapeake Bay, USA. As we attempted to apply this index to a study in the same region, we discovered the need to add more species; however, the scoring criteria were not defined well enough to do so. This study explicitly standardizes the scoring criteria and definitions and provides index scores for all waterbirds of the Chesapeake Bay. In addition, an alternative approach to estimate avian abundance is described, which allows for greater areal coverage compared to transect surveys. The utility of the modified index is then demonstrated with recent survey data of breeding and migratory waterbirds in Chesapeake Bay across a disturbance gradient. This explicitly-defined scoring system will facilitate application to new species in the Bay or new areas beyond this region. By providing these updates and analysis tools, this approach will be more accessible to new studies and regions, and provides a consistent methodology which can be applied across studies.This index when combined with other community integrity indices could provide a more powerful tool for estuarine managers.