Abstract: An experiment was conducted on the characteristics of root morphology and vitality, and soil microbial community diversity of three typical aquatic plants to determine their mitigation efficiency of agricultural non-point source pollutants in riparian buffer zones. All the aquatic plants used have significantly differences in the characteristics of root morphology and vitality. Root vitality values of the aquatic plants are in the following order: Iris pseudacorus > Acorus calamus > Lythrum salicaria. Root vitality has a significant correlation with root tip number. The aquatic plants show significant rhizosphere effect, soil microbial biomass in rhizosphere is markedly higher than that in bulk soils. Furthermore, microbial community in rhizosphere soils of the riparian buffer zone has the composition sequence as: bacteria > actinomycetes > fungi. Soil microbial community diversity index is as follows: I. pseudacorus > A. calamus > L. salicaria, having the same tendency as that of root vitality. The order of removal efficiency of TN, TP and COD_cr by the aquatic plants in the riparian buffer zone is I. pseudacorus > A. calamus > L. salicaria. The results suggest that variations in root vitality caused by differences in root structure of aquatic plants influence soil microbial community structure and diversity. This results in the differences in removal efficiencies of agricultural non-point source pollutants in riparian buffer zones.