I had trouble with dark stains on the bottom of our vinyl pool and the pool store suggested shocking and algaecide,which didn't help. It actually added additional areas of staining. Then I remembered muriatic acid and it was successful! When using muriatic acid, you should shut off your pump, so I do it in the evening. Also wear long pants, shoes and gloves, so you don't get any splashes on your skin and follow the manufactures directions on the container. Pour the muriatic acid around the pool perimeter, similar to when you add liquid shock. Keep your pump off for 12 hour or overnight and don't allow anyone to swim for 12 hours. In the morning, your stains should be gone. The pump should be started, vacuum the bottom and backwash. Muriatic acid can be purchased at Menards, Home Depot, Ace Hardware etc. for about $4.99 a gallon. I have a large 16' x 32' Doughboy pool with a deep end, so I have approximately 20,000 gallons of water. I added two gallons of muriatic acid. I hope this helps anyone with similar problems.