Embankments are common structures along rivers or lakes in riparian zones in plain areas. They should have natural slopes instead of slopes covered by concrete or other hard materials, in order to rebuild sustainable ecosystems for riparian zones. This study was conducted to evaluate the effects of vegetative slopes on water flow and pollutant transport through the embankments. Three embankments with different slope treatments (a bare slope, a slope covered in centipede grass, a slope covered in tall fescue) were examined, and three inflow applications of pollute water with different concentration of total nitrogen (TN) and total phosphorus (TP) used to simulate different agricultural non-point pollution levels. The results showed that the water flux rates of the three embankments were relatively stable under all inflow events, and almost all values were higher than 80%. The embankments with vegetative slopes had better nitrogen removal than the bare slope under all events, and the one with tall fescue slope was best, but the benefits of vegetative slopes decreased with increasing inflow concentration. Moreover, there were no significant differences between the embankments on phosphorus removal, for which the reductions were all high (above 90%) with most loads remaining in the front third of embankment bodies. Overall, the embankments with vegetative slopes had positive effects on water exchange and reducing non-point pollutant into lake or river water, which provides a quantitative scientific basis for the actual layout of lakeshores.