When you summon a lighting over the water on yourself, you can see that the lighting texture become invisible and it's "deletes" the water (shows texture under the water block(s) as if there was no water instead of lighting strike/white texture. 

How to reproduce:

1) Go over the lake or piece of water (around 1 - 3 blocks deep)
2) Use /summon lightning_bolt
3) You will see water texture & white lighting bold texture disappear for a split second and instead of those you will see ground below water