Treated effluent from wastewater treatment plants has become an important source of excess nutrients causing eutrophication in water. In this study, an ecological purification method was used to further treat eutrophic water. A three-season ecological purification scheme which comprised an emergent plant (Eme.), a submerged plant (Sub.) and a novel biological rope (Bio.), was designed for the treated effluent canal of a wastewater treatment plant. The removal parameters determined from the experiment were input into a QUAL2K model to simulate downstream water quality of the treated effluent canal. Respective removal rates of total nitrogen and total phosphorus of the Eme., Sub. and Bio. were 32.48–37.33% and 31.63–39.86% in summer, 14.12–33.61% and 17.74–23.80% in autumn, and 14.13–18.03% and 10.05–12.75% in winter, with 1-day reaction time. Optimal combinations for summer, autumn/spring, and winter are Eme. + Bio., Eme. + Bio. + Sub., and Sub. + Bio., respectively. Simulated load reduction rates of total nitrogen and total phosphorus for the treated effluent canal were 42.64–78.40% and 30.98–78.29%, respectively, year round with 2.5-day reaction time. This study provides an efficient evaluation and design method for ecological purification engineering.