Soil water percolation is an important process required to meet plant water needs, determine soil water storage, and affect soil water quality in riparian buffer strips. However, the effects of plant roots on soil percolation in riparian buffer strips are not totally understood, and contradictory results have been carried out on the effects of the root system on soil percolation rates. This study aimed to investigate soil percolation in natural grasslands and evaluate the relationships between root morphological characteristics and percolation rates. Path analysis was used to provide information on the relative contribution of root characteristics on soil percolation rates. Three mixed grasslands (Imperata cylindrica + Phragmites australis, I. cylindrica + Cynodon dactylon, and I. cylindrica + Juncellus serotinus) were selected in the Yellow River wetland natural reserves of Zhengzhou. Soil percolation rates (initial, average, and steady infiltration rates) were measured by using double-ring methods, and plant root morphological characteristics were analyzed. Soil percolation rates and plant root characteristic parameters of I. cylindrica + P. australis and I. cylindrica + C. dactylon were higher than those of I. cylindrica + J. serotinus. Initial percolation rate of I. cylindrica + P. australis and I. cylindrica + C. dactylon at 0–10 cm depth was 58.06% and 95.55% higher than that of I. cylindrica + J. serotinus, respectively. Percolation rates had a significant positive correlation with root characteristic parameters, and the main factor controlling soil percolation rates was root volume density (RVD). Mixed natural grasslands with more RVD improved soil infiltration and percolation rates.