Hybrid constructed wetlands (HCWs) are a promising solution for water ecology and environmental treatment, not only for conventional types of water pollution but also for antibiotics. Among the critical parameters for wetlands, the hydraulic loading rate (HLR) is especially important given the challenges of antibiotics treatment and frequent extreme rainfall. To investigate the removal performance of different HLRs on nutrients and antibiotics, as well as the response of antibiotics to nutrient removal, and the impact of HLRs on microbial communities, new HCWs with vertical flow constructed wetlands (VFCWs) and floating constructed wetlands (FCWs) in series were built. The results of the study showed that: (1) HCWs are highly effective in removing chemical oxygen demand (COD), NH4+−N, NO2−−N, and total phosphorus (TP) at low HLR (L_HLR), with removal efficiencies as high as 97.8%, 99.6%, 100%, and 80.5%. However, high HLR (H_HLR) reduced their removal efficiencies; (2) The average removal efficiency of fluoroquinolones (FQs) under different HLRs was consistently high, at 99.9%, while the average removal efficiency of macrolides (MLs) was 96.3% (L_HLR) and 88.4% (H_HLR). The removal efficiency of sulfonamides (SAs) was susceptible to HLRs, and the removal of antibiotics occurred mainly in the rhizosphere zone of wetland; (3) High concentrations of antibiotics in HCWs were found to inhibit and poison plant growth and to reduce the removal efficiency of TP by 12%. However, they had a minor effect on the removal efficiency of carbon and nitrogen nutrients; (4) H_HLR altered the diversity and abundance of microbial communities in different compartments of the wetland and also reduced the relative abundance of Bacillus, Hydrogenophaga, Nakamurella, Denitratisoma and Acidovorax genera, which are involved in denitrification and phosphorus removal processes. This alteration in microbial communities was one of the main reasons for the reduced performance of nitrogen and phosphorus removal.