Unoccupied aerial systems (UAS) have become common tools for ecological monitoring and management. However, UAS use has the potential to negatively affect wildlife. Both policy makers and practitioners require data about the potential impacts of UAS on natural biota, but few studies exist and some of the published results conflict. We conducted two experiments to assess the responses of chinstrap penguins (Pygoscelis antarcticus), Antarctic fur seals (Arctocephalus gazella), and leopard seals (Hydrurga leptonyx) to UAS overflights. First, to provide a baseline for assessing disturbance from UAS operations, we compare behavioral responses from UAS flights to those from traditional, ground surveys. Second, to inform users and policy makers about preferred flight methods, we assess behavioral and physiological responses to UAS flown at specific altitudes, during different stages of breeding chronology, and with other site factors. Between January 2017 and March 2018 we conducted 268 UAS flight approaches and 36 ground-based surveys at Cape Shirreff, Antarctic Peninsula. We applied generalized linear mixed effects models and Kruskal-Wallis tests to 10,164 behavioral scores obtained from three independent observers. When directly compared, behavioral responses by all species to UAS overflights at 30 m were not different from control periods, while responses to ground surveys were significantly more intense. Behavioral responses generally increased as UAS flew lower, and for penguins those increases intensified as the breeding season progressed (i.e., guard and molt stages). We argue that results from UAS wildlife response studies need to be assessed relative to the impacts of alternative methods, and within the ecological context of the target species. Finally, we suggest data-driven best practices for both UAS use and for the design of future UAS-wildlife response studies.