I have recently obtained a shellder and I have collected all the shards in my game. Do they come back or am I just out of water stones?
You can get evolution stones from Secret Super Training (You unlock that after you have fully trained a Pokemon) Also note: only fully trained Pokemon can do Secret Super Training.
You get water stones from:
Super Secret training (The Water Cup Begins
Secret Pals (ranger)
Fisherman Elliot rematches (5%)