PokéBase - Pokémon Q&A
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Thunder Stone Locations: Route 118, Route 124, New Mauville, Super Training and from Secret Pal in Secret Base

Water Stone Locations: Route 106, Route 124, Super Training and from Secret Pal in Secret Base

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If you play the highest rank of super training(you will need a max ev Pokémon to do this) the rounds there have a chance of giving stones upon completion.

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There is a collector on a small island on route 124. If you give him a shard* he will give you the corresponding stone.

*red shard=fire stone
blue shard=water stone
green shard=leaf stone
yellow shard=thunder stone

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