In many coastal regions throughout the world, there is increasing pressure to harden shorelines to protect human infrastructures against sea level rise, storm surge, and erosion. This study examines waterbird community integrity in relation to shoreline hardening and land use characteristics at three geospatial scales: (1) the shoreline scale characterized by seven shoreline types: bulkhead, riprap, developed, natural marsh, Phragmites-dominated marsh, sandy beach, and forest; (2) the local subestuary landscape scale including land up to 500 m inland of the shoreline; and (3) the watershed scale >500 m from the shoreline. From 2010 to 2014, we conducted waterbird surveys along the shoreline and open water within 21 subestuaries throughout the Chesapeake Bay during two seasons to encompass post-breeding shorebirds and colonial waterbirds in late summer and migrating and wintering waterfowl in late fall. We employed an Index of Waterbird Community Integrity (IWCI) derived from mean abundance of individual waterbird species and scores of six key species attributes describing each species’ sensitivity to human disturbance, and then used this index to characterize communities in each subestuary and season. IWCI scores ranged from 14.3 to 19.7. Multivariate regression model selection showed that the local shoreline scale had the strongest influence on IWCI scores. At this scale, percent coverage of bulkhead and Phragmites along shorelines were the strongest predictors of IWCI, both with negative relationships. Recursive partitioning revealed that when subestuary shoreline coverage exceeded thresholds of approximately 5% Phragmites or 8% bulkhead, IWCI scores decreased. Our results indicate that development at the shoreline scale has an important effect on waterbird community integrity, and that shoreline hardening and invasive Phragmites each have a negative effect on waterbirds using subestuarine systems.