To sustain frog populations, it is important to conserve favorable aquatic habitats. In Japan, rice paddies play an important role as breeding habitat for frog species; however, environmental changes and abandonment of rice paddies have led to declining frog populations. In this study, we conducted surveys at various aquatic habitats in a yatsuda area in the Sayama Hills to determine the characteristics of rice paddies under different management systems, and the breeding habitat preferences and favorable aquatic habitats for Japanese brown frog (Rana japonica) eggs. We found 134 egg masses at 14 study sites, and monitored them until they hatched, died, or were lost, and also recorded environmental factors, such as water temperature and depth. First, we conducted principal component analysis to determine the study site characteristics, and second, we constructed generalized additive mixed models to investigate the relationship between environmental factors and the number of new egg masses, hatching success rate, and number of days to hatch. Our results showed no clear pattern of how environmental factors changed after rice paddy abandonment, except for an increase in vegetation cover over rice paddies. Conversely, our results showed R. japonica breeding habitat preference and egg hatching success were related to various aspects of aquatic habitats. Our investigation revealed the preferred breeding habitat for R. japonica and provides key information for developing practical conservation measures regarding the overall management of rice paddies, such as irrigation and mowing, to sustain R. japonica populations in yatsuda areas.