Bioacoustics monitoring has become increasingly popular for studying the behavior and ecology of vocalizing birds. This study aims to verify the practical effectiveness of localization technology for auditory monitoring of endangered Eurasian bittern (Botaurus stellaris) which inhabits wetlands in remote areas with thick vegetation. Their crepuscular and highly secretive nature, except during the breeding season when they vocalize advertisement calls, make them difficult to monitor. Because of the increasing rates of habitat loss, surveying accurate numbers and their habitat needs are both important conservation tasks. We investigated the feasibility of localizing their booming calls, at a low frequency range between 100–200 Hz, using microphone arrays and robot audition HARK (Honda Research Institute, Audition for Robots with Kyoto University). We first simulated sound source localization of actual bittern calls for microphone arrays of radii 10 cm, 50 cm, 1 m, and 10 m, under different noise levels. Second, we monitored bitterns in an actual field environment using small microphone arrays (height = 12 cm; width = 8 cm), in the Sarobetsu Mire, Hokkaido Island, Japan. The simulation results showed that the spectral detectability was higher for larger microphone arrays, whereas the temporal detectability was higher for smaller microphone arrays. We identified that false detection in smaller microphone arrays, which was coincidentally generated in the calculation proximate to the transfer function for the opposite side. Despite technical limitations, we successfully localized booming calls of at least two males in a reverberant wetland, surrounded by thick vegetation and riparian trees. This study is the first case of localizing such rare birds using small-sized microphone arrays in the field, thereby presenting how this technology could contribute to auditory surveys of population numbers, behaviors, and microhabitat selection, all of which are difficult to investigate using other observation methods. This methodology is not only useful for the better understanding of bitterns, but it can also be extended to investigate other rare nocturnal birds with low-frequency vocalizations, without direct ringing or tagging. Our results also suggest a future necessity for a robust localization system to avoid reverberation and echoing in the field, resulting in the false detection of the target birds.