Water management and crop rotation influence aquatic biodiversity in rice paddies

Irrigation timing and crop rotation strongly influence aquatic biodiversity of rice paddies. Species with seasonal reproduction or soil-dormant stages are especially sensitive to hydroperiod shifts. However, the ecological consequences of delayed transplanting and double-cropping, increasingly adopted under climate and economic pressures, remain underexplored. Aquatic animal communities were investigated across 39 paddy fields in Saitama Prefecture, Japan, under three regimes differing in transplanting timing and crop rotation: early transplanting, normal season, and wheat–rice double-cropping. Each paddy was surveyed three times during the growing season. Generalized linear mixed models, permutational multivariate analysis of variance, and local contributions to beta diversity (LCBD) metrics were used to assess community composition, richness, and abundance. Results showed that early transplanting fields favored amphibians, loaches, and drought-tolerant invertebrates, whereas double-cropping paddies harbored prey-rich communities with high densities of chironomid larvae and predatory insects. These regimes also had significantly higher LCBD values, indicating greater contributions to landscape-scale beta diversity. Indicator analysis showed reproductive timing and drought tolerance explained species–regime associations. These findings highlight how agricultural practices, albeit confounded with regional and interannual variation, function as ecological filters shaping aquatic biodiversity at local and regional scales. As climate change drives shifts in transplanting schedules, water-management strategies that preserve early-season aquatic habitats (e.g., maintaining early flooded paddies or providing alternative shallow water habitats) are critical for sustaining biodiversity and ecosystem services in rice-based agroecosystems across temperate and subtropical Asia.