you have to dive underwater by sootopolis city and you have to go in the little cave underwater where youll find the sud and then you surface there.
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you will find team aqua in the under water cavern near the dive point in sootopolis
in the back of the base, but they get away with it.
team aqua and team magma, u have to beat them both as opposed to ruby and Sapphire where u only have to beat the team that is the same color of your game(ruby=magma)(Sapphire=aqua)
The Team Aqua boss is in the Team Aqua Hideout northeast of Lilycove City. You will need the HM move Surf to reach the hideout.
At a cave under water in route 128 :)