Responses of aquatic biodiversity to irrigation timing and double-cropping regimes in rice paddies

• Aquatic communities from 39 rice paddies were surveyed under three management regimes. • Early transplanting favored amphibians, loaches, and drought-tolerant invertebrates. • Wheat–rice double-cropping supported prey-rich chironomid larvae and predatory insects. • Both regimes disproportionately contributed to landscape-scale beta diversity. • Irrigation timing and double-cropping shape aquatic communities. Irrigation timing and double-cropping strongly influence aquatic biodiversity in rice paddies, serving as key management drivers that can be incorporated into biodiversity‐monitoring frameworks. Species with seasonal reproduction or soil-dormant stages are especially sensitive to hydroperiod shifts. However, the impacts of delayed irrigation and double-cropping on paddy ecosystems, increasingly adopted under climate and economic pressure, remain underexplored. I surveyed aquatic animal communities in 39 paddies in Saitama Prefecture, Japan, under three regimes: early transplanting, normal-season, and double-cropping (rice transplanted after wheat harvest). Generalized linear mixed models (GLMMs), permutational multivariate analysis of variance (PERMANOVA), and local contributions to beta diversity (LCBD) were used to assess community structure. Early transplanting fields favored amphibians, loaches, and drought-tolerant invertebrates, whereas double-cropping paddies harbored prey-rich communities dominated by chironomid larvae and predatory insects. Both regimes also had higher LCBD values, indicating greater contributions to landscape-scale beta diversity. These results highlight irrigation timing and double-cropping as key management drivers shaping aquatic biodiversity in rice agroecosystems. As climate change alters irrigation schedules, incorporating these management practices into biodiversity monitoring frameworks will be critical for sustaining biodiversity and ecosystem services, since irrigation timing and cropping systems are readily measurable management variables.