<p>Anammox bacteria play an important role in the nitrogen cycle within freshwater ecosystems. However, it is not yet known how their communities in floodplain lakes respond to hydrological regime changes. This research focused on the surface sediments of Poyang Lake, China’s largest floodplain lake. We employed high-throughput sequencing and quantitative polymerase chain reaction (qPCR) methods to analyze the variations in the alpha diversity, abundance, community structure, and co-occurrence network of anammox bacteria in different hydrological regimes (wet, normal, and dry phases). The results showed that there were no significant differences in the alpha diversity indices (except for the Chao richness estimator) among hydrological phases. The abundance and community structure of anammox bacteria varied significantly across hydrological regimes. In the dry phase, the average abundance of anammox bacteria decreased by 68.1% and 66.6% compared to the wet and normal phases, respectively. Among the 34 main operational taxonomic units (OTUs) of the anammox bacterial communities, 26 OTUs showed significant differences in the relative abundance between different hydrological regimes. Co-occurrence network analysis revealed that the internal connections among anammox bacterial species were the closest in the dry phase, followed by the wet phase, and the weakest in the normal phase. Total nitrogen, total phosphorus, and organic matter were the primary environmental factors influencing the abundance and community structure of anammox bacteria. This study enhances our understanding of the ecological impacts of the hydrological regime and the anammox process in floodplain lakes.</p>