Water eutrophication is one of the most serious environmental problems in urban lakes and ponds due to the excessive nutrients. To deal with this problem, the development of methods for supporting ecological rehabilitation has been undertaken. Meanwhile, the trophic interactions during rehabilitation also have been analyzed. In this study, a new technique was employed to solve the water eutrophication problems in an urban pond. To evaluate the water eutrophication at a pilot scale, an enhanced artificial floating-type biological treatment system (FBTS) composed of a floating bed, macrophyte, artificial biofilm carrier (polyurethane sponge) and aerator could be used as equipment for urban pond remediation. In addition, FBTS was employed to decrease the total nitrogen (TN), ammonia-nitrogen (NH3-N), total phosphorus (TP) and chemical oxygen demand (COD) in water. Meanwhile, the changes of water qualities were monitored in the remediation process, and differences in phytoplankton functional group diversity were also registered. Cyanobacteria would decrease after the removal of P, and the diatom assemblage composition changed. The dominant species Cyanophyta were transformed to co-existed with Bacillariophyta, Pyrrophyta and Chlorophyta due to the improvement of water quality. Consequently, this new FBTS could be a promising eco-technology for the removal of nitrogen and phosphorus from eutrophic water, and even could promote the phytoplankton succession.