Successful refueling at staging sites is essential for the survival and reproduction of migratory birds. Understanding their staging ecology is therefore crucial for the conservation of migrant species. Rice fields in the mid-western region of the Korean Peninsula serve as staging habitats for the black-tailed godwit (Limosa limosa). We examined the behavior of staging black-tailed godwits in rice fields located in the East Asian-Australasian Flyway during their northward migration. Specifically, we tested the effect of flock size and water level on the foraging, vigilance, and resting behaviors of black-tailed godwits. Our observations revealed that as flock size increased, stepping rate, pecking rate, and vigilance duration decreased, while probing rate, preening duration, and foraging efficiency increased. Stepping and pecking rates increased at low water levels, compared with high water levels. We determined that the behavior of black-tailed godwits at the staging site is influenced by flock size and water level. These observations suggest that black-tailed godwits form larger flocks to increase foraging efficiency by lowering individual-level vigilance, and to spend more time on preening, which is critical for flight and survival. It can be also inferred, based on the shift in primary foraging mode between probing and pecking depending on the water level, that they obtain higher foraging efficiency by flexibly adapting their foraging mode to the conditions in rice fields that are subject to agricultural activities. Our results are expected to serve as basic data for establishing efficient management strategies for anthropogenic habitats for the conservation of migratory shorebirds such as black-tailed godwit.