Water overflowing from a levee generates scour holes on the toe, which progresses towards the backward crest of the levee and results in nappe flow generation. The direct collision of nappe flow on the downstream area causes levee failure. It is important to introduce a novel countermeasure against scouring caused by nappe flow. Hence, the present study utilized a new technique to reduce scouring due to nappe flow by introducing a combination of pooled water and geogrids. Herein, laboratory experiments were conducted with the three cases for rigid bed (R), named as NR, G1R, G2R (N, G1 and G2 represent no geogrid, geogrid 1 and geogrid 2, respectively), and moveable bed (M), named as NM (nothing moveable), G1M (geogrid 1 moveable), G2M (geogrid 2 moveable), to elucidate the effect of dimensionless pooled water depth (DP*), overtopping depth (DC*) and the aperture size of geogrids (d*) on flow structure and scouring. The results showed that the scour depth was reduced by around 17–31% during the NM cases, 57–78% during the G1M cases and 100% during the G2M cases by increasing the DP* from 0.3 to 0.45. Hence, the combination of geogrids with pooled water (G1M, G2M) performed a vital role in suppressing the scouring, but the results of G2M were more advantageous in terms of scouring countermeasures.