Unoccupied aerial systems (UASs) may provide cheaper, safer, and more accurate and precise alternatives to traditional waterfowl survey techniques while also reducing disturbance to waterfowl. We evaluated availability and perception bias based on machine-learning-based non-breeding waterfowl count estimates derived from aerial imagery collected using a DJI Mavic Pro 2 on Missouri Department of Conservation intensively managed wetland Conservation Areas. UASs imagery was collected using a proprietary software for automated flight path planning in a back-and-forth transect flight pattern at ground sampling distances (GSDs) of 0.38–2.29 cm/pixel (15–90 m in altitude). The waterfowl in the images were labeled by trained labelers and simultaneously analyzed using a modified YOLONAS image object detection algorithm developed to detect waterfowl in aerial images. We used three generalized linear mixed models with Bernoulli distributions to model availability and perception (correct detection and false-positive) detection probabilities. The variation in waterfowl availability was best explained by the interaction of vegetation cover type, sky condition, and GSD, with more complex and taller vegetation cover types reducing availability at lower GSDs. The probability of the algorithm correctly detecting available birds showed no pattern in terms of vegetation cover type, GSD, or sky condition; however, the probability of the algorithm generating incorrect false-positive detections was best explained by vegetation cover types with features similar in size and shape to the birds. We used a modified Horvitz–Thompson estimator to account for availability and perception biases (including false positives), resulting in a corrected count error of 5.59 percent. Our results indicate that vegetation cover type, sky condition, and GSD influence the availability and detection of waterfowl in UAS surveys; however, using well-trained algorithms may produce accurate counts per image under a variety of conditions.