Small unmanned aircraft systems present an emerging technology with the potential to survey colonial waterbird populations while reducing disturbance in comparison to traditional ground counts. Recent research with these systems has been performed on some colonially nesting avian species; however, none have focused on wading bird species. During 2015–2016, this study tested the behavioral response of a mixed-species rookery (Cattle Egret (Bubulcus ibis), Snowy Egret (Egretta thula), Glossy Ibis (Plegadis falcinellus) and a groundnesting colony of Common Terns (Sterna hirundo)) in shrub habitat to small unmanned aircraft system flights at 12 m, 15 m, 30 m, and 50 m. Even at the lowest altitudes, the birds either showed no reaction or acclimated within 60 sec of the fly-over. Conversely, physically entering the colony to conduct ground surveys resulted in all Common Terns flushing from their nests beginning when the observer was 50 m away and required significantly more time in the colony overall: ~30–60 min vs. ~3–7 min with the small unmanned aircraft system. While this study focuses only on the behavioral response of nesting birds and not comparison of count estimates, these results provide preliminary evidence that small unmanned aircraft systems provide the potential to monitor colonial nesting bird populations while minimizing disturbance to the colony.