If Sanctum of Calm Waters leaves the battlefield while its ability is on the stack, you may control no Shrines as the ability resolves. If so, you may choose to draw zero cards and discard one, or you may choose not to draw zero cards and not discard a card.

Each Shrine has an ability that counts the number of Shrines you control. These abilities include the Shrine they're printed on.

Shrines count only enchantments with the subtype Shrine. Other cards with “shrine” in their name (such as Jungle Shrine, Luxa River Shrine, and Nantuko Shrine) don't count.

You draw X cards and discard a card all while the triggered ability is resolving. Nothing can happen between the two, and no player may choose to take actions.