The emergent, floating leaf and submerged plants were integrated into Staged Ecological Floating-beds (SEF) for malodorous river′s purification and remediation. The dynamic characteristics of phytoplankton and the water quality were monitored to study the mechanisms of the ecological staged floating-beds for remediation of malodorous river. The results showed that the percentage of Chlorophyta and Cyanophyta decreased after SEF remediation. It was also found that the dominant phytoplankton species were changed, indicating that the quality of effluent were improved. The phytoplankton density reached the maximum in September and the lowest in June, with their values higher than 1×105ind.·L-1 reflecting the high concentrations of nutrients in water. Emerged plant floating-beds among the SEF have the lowest phytoplankton density, indicating that the Hydrocotyle vulgaris has the strongest growth inhibition on algae. Additionally, three kinds of bio-diversity indexes of phytoplankton showed the trends of water quality were improved notably, but there were significant differences in these indexes, and that means it is not suitable to assess the water quality by a single index. The phytoplankton species had close correlation with CODCr and the phytoplankton density had the same relationship with DO. The Shannon-Wiener diversity index was highly correlated with CODCr. The Margalef index was also correlated with CODCr and pH, and the Pielou index significantly correlated with TP ( r =0.438, P 0.05). However, all indexes correlated with NH3-N were not remarkable.