We examined monthly occurrence patterns and feeding habits of larvae and juveniles of the critically endangered Ryukyu-ayu Plecoglossus altivelis ryukyuensis in the lower reach of the Kawauchi River, Amami-oshima Island, southern Japan, for two successive years. The study area was classified into a brackish lake (Lake Uchiumi) and a coastal zone (Sumiyo Bay) based on monthly variations in water temperature and salinity. Larvae and juveniles occurred from December to April in the first year and from January to February in the second year, respectively. Smaller-sized and earlier developmental-staged P. altivelis ryukyuensis individuals tended to emerge in larger numbers in Lake Uchiumi than in Sumiyo Bay. The present data suggest that Lake Uchiumi, where the physical environment is characterized by lower temperature and salinity than in Sumiyo Bay, would be suitable as a nursery ground for this fish, especially for earlier developmental-staged larvae. No individuals ≥25.0 mm body length, which is the size at which they begin their upstream migration, occurred in Lake Uchiumi or Sumiyo Bay in April or May, when upstream migration is assumed to reach a peak based on previous studies, in either year. The peak of upstream migration, therefore, may have occurred several months earlier in the years covered in this study due to higher water temperature than in typical years. To assess the feeding habits of this fish, the gut contents were observed. In both areas, copepods were abundant in P. altivelis ryukyuensis diet with calanoids and Oithona spp. being the most abundant. The diet composition differed between Lake Uchiumi and Sumiyo Bay and clearer ontogenetic variation in the composition of the diet was observed in Lake Uchiumi. Small individuals fed on tintinnid ciliates, but the proportion of these organisms in the diet gradually decreased with growth. Large individuals fed exclusively on harpacticoid copepods and insects including demersal species. Overall, larval and juvenile P. altivelis ryukyuensis exhibited a generalist feeding habit that tended to increase with growth. It is indispensable to adequately manage the environmental conditions in the lower reach of the Kawauchi River, especially Lake Uchiumi, to conserve P. altivelis ryukyuensis population.