A new type of sediment microbial fuel cell (SMFC) with floating macrophyte Limnobium laevigatum, Pistia stratiotes, or Lemna minor L. biocathode was constructed and assessed in three phases at different hydraulic retention time (HRT) for electrical current generation during the degradation of urban river sediment. The results showed a highest voltage output of 0.88 ± 0.1V, maximum power density of 80.22mWm-3, highest columbic efficiency of 15.3%, normalized energy recovery of 0.030kWhm-3, and normalized energy production of 0.005kWhm-3 in the Lemna minor L. SMFC during phase 3 at HRT of 48h, respectively. Highest removal efficiencies of total chemical oxygen demand of 80%, nitrite of 99%, ammonia of 93%, and phosphorus of 94% were achieved in Lemna minor L. system, and 99% of nitrate removal and 99% of sulfate removal were achieved in Pistia stratiotes and Limnobium laevigatum system during the SMFC operation, respectively. Pistia stratiotes exhibited the highest growth in terms of biomass and tap root system of 29.35g and 12.2cm to produce the maximum dissolved oxygen of 16.85 ± 0.2mgL-1 compared with other macrophytes. The predominant bacterial phylum Proteobacteria of 62.86% and genus Exiguobacterium of 17.48% were identified in Limnobium laevigatum system, while the class Gammaproteobacteria of 28.77% was observed in the control SMFC. The integration of technologies with the continuous flow operation shows promising prospect in the remediation of polluted urban river sediments along with the generation of electrical current.