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
Source
Hopefully I've Helped!
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.
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
