If if its a lower level like 10-20 you should probably go to the cave on the mountain where you fight team aqua.
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Best non-legendary water pokemon would be Gyarados. Best legendary water pokemon is Kyogre.
There is only one pokemon you can use it on and that is eevee to get vaporeon
there is not one in sapphire emerald or ruby only in firered leafgreen and water
It is because you have awoken the three Regis:Regirock,Regice,and Registeel.
In the sea, where the water is darker than the surrounding areas.