In Japan, rice paddies have acted as substitute habitats for pond-breeding frogs. However, frog populations are declining due to the loss of habitat and environmental changes in rice paddy areas. Frogs need both aquatic and terrestrial habitats to complete their life history; in rice paddy areas, levees that surround rice paddies provide terrestrial habitats for basking, foraging, and shelter from predators. Studying microhabitat use at levees is important to elucidating the ecological roles of levees and to properly managing them to support frog populations. In this study, we conducted surveys in lowland modernized rice paddy areas in Shiga Prefecture in which a common species, Hyla japonica, and an endangered species, Pelophylax porosa brevipoda, were found. We captured frogs at levees and recorded environmental factors related to levee vegetation, rice paddy conditions, and weather. We constructed generalized linear mixed models to examine the effects of environmental factors on juvenile and adult H. japonica and on small and large juveniles, females, and males of P. p. brevipoda. Our results showed distinct microhabitat uses at levees in different species, sexes, and body sizes. In general, abundance was high at levees with vegetation that provided shelter. The water depth in rice paddies negatively influenced juvenile H. japonica and large juvenile and small female P. p. brevipoda, and positively influenced small male P. p. brevipoda. The maintenance of a mosaic structure of levees was important not only to support frog populations but also to maintain frog diversity in the area.