the strongest water Pokemon is Palkia
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Reshiram. But if you make any other Pokemon stronger than it by level, yes, then it will be that Pokemon. But if you look to it by the side of legends and legendary power, it is Reshiram.
Mewtwo, a Pokemon born for fighting, is the strongest in Yellow. It's Pyschic, legendary, and a man-made copy of Mew.
Best non-legendary water pokemon would be Gyarados. Best legendary water pokemon is Kyogre.
The strongest dragon type in pokemon Emerald, Sapphire and Ruby, is the legendary pokemon Rayquaza. In terms of non-legendary pokemon, both salamance and flygon are strong dragon types.
arceusKyogre is the strongest water type Pokémon.