"The annual mean, representative of the current state of the Nile, is 1.4 × 103 m3 s−1" [1,400 cubic meters per second] River Discharge into the Mediterranean Sea
"the plant is expected to have the capacity to purify 164,000 cubic meters of seawater each day. "
IOW, a water plant utilizing Nile water and yielding 164,000 m3 water per day would consume the entire flow of the Nile for two whole minutes each day. About 0.14%
Yeah, but it ain't just this one plant that draws (or could potentially draw) from the Nile. The Nile has to have a certain minimum (and large) flow to remain a viable means of transportation. So the actual amount that can be tapped is much smaller than the figure you are quoting.