Development of wind energy facilities results in interactions between wildlife and wind turbines. Raptors, including bald and golden eagles, are among the species known to incur mortality from these interactions. Several alerting technologies have been proposed to mitigate this mortality by increasing eagle avoidance of wind energy facilities. However, there has been little attempt to match signals used as alerting stimuli with the sensory capabilities of target species like eagles. One potential approach to tuning signals is to use sensory physiology to determine what stimuli the target eagle species are sensitive to even in the presence of background noise, thereby allowing the development of a maximally stimulating signal. To this end, we measured auditory evoked potentials of bald and golden eagles to determine what types of sounds eagles can process well, especially in noisy conditions. We found that golden eagles are significantly worse than bald eagles at processing rapid frequency changes in sounds, but also that noise effects on hearing in both species are minimal in response to rapidly changing sounds. Our findings therefore suggest that sounds of intermediate complexity may be ideal both for targeting bald and golden eagle hearing and for ensuring high stimulation in noisy field conditions. These results suggest that the sensory physiology of target species is likely an important consideration when selecting auditory alerting sounds and may provide important insight into what sounds have a reasonable probability of success in field applications under variable conditions and background noise.