This data set is comprised of five files related to the modification and scoring of Index of Waterbird Community Integrity (IWCI) scores for all waterbirds of the Chesapeake Bay. One Excel file (A) contains a list of 100+ Chesapeake waterbird species and their species attribute and IWCI scores. Another Excel file (B) contains case study data from recent surveys of breeding and migratory waterbirds in Chesapeake Bay and shoreline delineations across a disturbance gradient that were used to demonstrate the utility of the modified index. Finally, three supplemental files include an Access database (C), R code (D) and a protocol (E) for running the complex steps to calculate index scores.