In recent decades, there has been increasing interest in the application of ecological indices to assess ecosystem condition in response to anthropogenic activities. An Index of Waterbird Community Integrity was previously developed for the Chesapeake Bay, USA. However, the scoring criteria were not defined well enough to generate scores for new species that were not observed in the original study. The goal of this study was to explicitly define the scoring criteria for the existing index and to develop index scores for all waterbirds of the Chesapeake Bay. The standardized index then was applied to a case study investigating the relationship between waterbird community integrity and shoreline development during late summer and late fall (2012–2014) using an alternative approach to survey methodology, which allowed for greater area coverage compared to the approach used in the original study. Index scores for both seasons were negatively related to percentage of developed shorelines. Providing these updated tools using the detailed scoring system will facilitate future application to new species or development of the index in other estuaries worldwide. This methodology allows for consistent cross-study comparisons and can be combined with other community integrity indices, allowing for more effective estuarine management.