Hydrological conditions determine the assembly processes of zooplankton in the largest Yangtze River-connected Lake in China

•Water age, crucial in shaping Poyang Lake’s zooplankton diversity.•Floods alter zooplankton dispersal in China’s largest lake.•Environmental DNA reveals zooplankton diversity in China’s largest freshwater lake.•Water age and total nitrogen identified as key factors in zooplankton community composition. In floodplain lakes, alterations in hydrological conditions can lead to changes in the structure of aquatic communities, potentially affecting biodiversity. Despite their critical role, the influence of specific hydrological and ecological factors on zooplankton community assembly and diversity remains poorly understood. We employed various methods to clarify how aquatic communities assemble and maintain diversity in these habitats. We calculated water age with the Environmental Fluid Dynamics Code (EFDC) and identified zooplankton using environmental DNA (eDNA) technology. We used these data to explore the relationship between zooplankton assembly, water age, and other ecological factors in Poyang Lake, China’s largest freshwater lake. We identified 1,142 operational taxonomic units (OTUs), mainly from Rotifera and Copepoda, representing the zooplankton community. The main driving factors for community differences were water age and total nitrogen. Water age ranged from 179 days to less than 1 day, with substantial spatial differences increasing from the western to the eastern region, particularly during the flood period (April-October). Spatial heterogeneity in other environmental factors, such as total nitrogen, dissolved organic carbon, and chlorophyll-a, also significantly impacted the zooplankton community composition. The assembly of the zooplankton community in Poyang Lake was primarily influenced by homogeneous selection, dispersal limitation, and ecological drift. During the flooding season, strong hydrodynamic forces created quick flush conditions that increased dispersal limitations, affecting the assembly process. Additionally, homogeneous selection played a major role in shaping community composition in seasonally inundated alluvial lands. This study found that water age, total nitrogen, dissolved organic carbon, and chlorophyll-a all contribute to intra-lake differences in the assembly processes of zooplankton communities in floodplain lakes. These findings improve our understanding of floodplain lake ecology, offering valuable insights for conservation biodiversity in floodplain lake.