U don't go through the waterfall, u go over the waterfall. The goal is to have the HM waterfall. This HM allows ur Pokemon to climb the waterfall.
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You go to where the girl (Jasmine) is under the Gym on the beach and she will give you Waterfall (the HM obviously. You surf on the water behind her and when you get to the waterfall use waterfall, then go through Victory Road, and Then face the Pokemon League.
you do need hm waterfall for mt. conet.There's a waterfall in mt.conet
go to the bottom of the waterfall at the Pokemon league.
you can use waterfall in victory road and at the end when you are finished with victory road
beat volkner then talk to jasmine.