Unmanned aerial vehicles (UAVs) have become a popular wildlife survey tool. Most research has focused on detecting wildlife using UAVs with less known about behavioral responses. We compared the behavioral responses of breeding blue-winged teal (Spatula discors) (n = 151) and northern shovelers (Spatula clypeata) (n = 46) on wetlands flown over with a rotary DJI Matrice 200 quadcopter and control wetlands without flights. Using a GoPro camera affixed to a spotting scope, we conducted focal individual surveys and recorded duck behaviors for 30 minutes before, during, and 30 minutes after UAV flights to determine if ducks flushed or changed in specific activities. We also conducted scan surveys during flights to examine flushing and movement on the entire wetland. Between 24 April and 27 May 2020, we conducted 42 paired (control and flown) surveys. Both teal and shovelers increased proportion of time engaged in overhead vigilance on flown wetlands from pre-flight to during flight (0.008 to 0.020 and 0.006 to 0.032 of observation time, respectively). Both species left the wetland more frequently during flights than ducks on control wetlands. Despite similarities between species, we observed marked differences in time each species spent on active (e.g., feeding, courtship, swimming), resting, and vigilant behaviors during flights. Overall, teal became less active during flights (0.897 to 0.834 of time) while shovelers became more active during this period (0.724 to 0.906 of time). Based upon scan surveys, ducks flushed in 38.1% of surveys while control wetlands only had a single (2.4%) flush during the flight time. We found launch distance was the most important predictor of whether ducks swam for cover or away from the UAV which could result in inaccurate counts. Ducks appear aware of UAVs during flights, but minimal behavioral shifts suggest negative fitness consequences are unlikely.