Submerged macrophytes are capable of inhibiting algae growth and removing nutrients from water with cost-effective and ecofriendly properties. The purification efficiency of three submerged macrophytes (Ceratophyllum demersum, Myriophyllum spicatum, and Vallisneria natans) was systematically compared in submerged macrophyte ponds (SMPs). Twelve SMP reactors divided into three groups were constructed to treat synthetic eutrophic wastewater throughout the summer and autumn season. The results demonstrated that higher macrophyte density could promote water purification performance. Summer tests exhibited better removal performance than autumn tests. Based on comprehensive consideration, constructing high-quality-concentration Myriophyllum spicatum pond in summer season was the optimal design and operation of SMPs, in which 43.8±2.0% TN, 97.8±1.0% TP, 99.0±1.0% DCOD, and 68.7±3.0% algae biomass could be reduced.