The performance of different suspended fillers (zeolite, drinking water treatment residual, biochar, woodchip and stereo-elastic packing) and their combinations in treating municipal wastewater in ecological floating beds (Eco-FBs) planted with Myriophyllum aquaticum was assessed. Six sets of enhanced Eco-FBs were developed to assess the individual and synergistic effects of combinations of the various fillers and microorganisms on nutrient elimination. The results demonstrated mean TN, NH4-N, TP and COD purification efficiencies of 99.2 ± 11.2 %, 99.82 ± 16.4 %, 98.3 ± 14.3 %, and 96.1 ± 12.3 %, respectively in the Eco-FBs strengthened with all five fillers. The corresponding purification rates were 0.89 ± 0.14, 0.75 ± 0.12, 0.08 ± 0.016, and 7.05 ± 1.09 g m−2 d−1, which were 2–3 times higher than those of the conventional Eco-FB system. High-throughput sequencing showed that some genera related to nutrient transformation, including Proteobacteria (24.13–51.95 %), followed by Chloroflexi (5.64–25.01 %), Planctomycetes (8.48–14.43 %) and Acidobacteria (2.29–11.65 %), were abundantly enriched in the strengthened Eco-FBs. Enhancement of the Eco-FBs with various fillers significantly increased microbial species richness and diversity as demonstrated by Chao1, Shannon and Simpson's indexes, particularly when all the five fillers were combined. Therefore, introducing suspended fillers into Eco-FBs is an appropriate approach for improving nutrient elimination from municipal wastewater.