You need to go inside a cave where you will verse team aqua or team magma (can't remember which one). When you win they will move. PS: This is my first question I have answered, tell me how I went!
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You must defeat Team Aqua in their Lilycove City base (right next to the Wailmers). To gain entrance to the base, you must first go to Mt. Pyre and climb to the summit.
From Fortree City, travel south-east and then east to Lilycove City. You will find some wailmers blocking the sea in the Eastern part at the Beach. Fly/Travel to Slateport and go to either Slateport Harbor or Stern's Shipyard to find a lot of people. Talk to the one getting filmed by a camera crew, then go back to Lilycove City and use Surf to get in the cave nearby the Wailmers.
surf to mount pyre then beat team aqua/magma then you can surf to team aquas hideout from lylicove after that the wailmers wil move and you can surf to modsep
You have to go to the hideout of team aqua which is in lilycove and beat everybody. then, when u come out, they will be gone.
If your talking about the wailmers in Lilycove city then you'll hafta go into the cave that is just north of them and defeat team Magma/Aqua. Then you might hafta fite Groudon/Kyogre. After that they shud have moved ;]