The configuration of water depth (WD) and flow velocity (FV) in floating constructed wetlands (FCWs) reflects the complex interactions between hydraulic conditions and wastewater treatment performance. Properly configuring hydraulic conditions can optimize performance. This study explored the removal and degradation of organic matter and nitrogen (N) in FCWs with three different WDs (50 cm (SD), 70 cm (MD), and 95 cm (DD)) under four FV conditions (0, 0.3, 1.0, and 1.5 m/d). It also analyzed the regulatory effects of hydraulic conditions on microbial community structure to provide new insights for configuring hydraulic conditions in FCWs. The results indicate that variations in WD and FV do not significantly affect COD removal (p > 0.05), with removal efficiency (RE) consistently reaching 90 % across all conditions. However, hydraulic conditions do influence the degradation rate (k) of COD, with increased FV enhancing the k in MD and DD. In contrast, WD significantly impacts the removal of NH4+−N (p < 0.05), with RE in SD exceeding 80 % across all four FVs. The primary reason is that increased WD reduced the abundance of nitrifying bacteria (Nitrosomonas and Nitrospira) and functional genes (hao and pmoABC-amoABC). Meanwhile, increased WD and FV significantly enriched the denitrifying bacteria genera (such as Massilia, Bacillus, Ensifer, and Rhodobacter) and certain functional genes (nap and nir), favoring the denitrification process and enhancing the dissimilatory nitrate reduction to ammonium (DNRA) process. Furthermore, microbial community diversity, richness, and the number of operational taxonomic units (OTUs) were highest in SD, but decreased with increased WD. This is mainly related to changes in oxygen (O2) transmission and nutrient concentration. These findings help us understand the mechanisms by which hydraulic regulation affects the removal of organic matter and N in FCWs. They also propose potential solutions from a hydraulics perspective to enhance N removal.