Ruby/Sapphire/Emerald:
~There's one in the abandoned ship from what I can remember.
~If you dive in the diving spots, some lead to areas with shards. Find a blue shard and give it to the shard hunter in his house located between Lilycove and Mossdeep, and he'll give you a water stone.
~You can also find blue shards off wild Clamperl.
Fire Red/Leaf Green:
~You can purchase water stones at the Celedon City department store, for like 2,500 or something, at the fourth or fifth floor. (Can't remember exactly)