Adam Clarke on Psalms 89:9

Thou rulest the raging of the sea - Whoever has seen the sea in a storm, when its waves run what is called mountain high, must acknowledge that nothing but omnipotent power could rule its raging.

When the waves thereof arise, thou stillest them - Thou governest both its flux and reflux. Thou art the Author of storms and calms. There may be a reference here to the passage of the Red Sea, and the strong wind that agitated its waves at that time; as the next verse seems to indicate.