Since the water went back up, drop by drop as it had fallen, I at first assumed that Granny used a time-reversal spell. If she had just used magic to remove it, it would have been gone all at once. But it seems odd that she would have used magic at all, given that Granny prefers to use ordinary methods even for much harder work than cleaning up a spill.
So maybe it wasn't that Granny used magic. Maybe it was that the cottage itself has a degree of magic that is somehow charged up by being the residence of a witch, and when the witch is gone, the cottage runs down, like the clock. [Or, in a different story, like the staff of a wizard, which is a reservoir for magic that the wizard can use but must recharge.] When a witch returns, the cottage begins to regain its magical protection, or is charged, and the damage is reversed.
Maybe Granny wasn't using a specific spell, but she has an ability to make natural phenomena act in ways independent of the way it usually does--almost respecting her power without her needing to actually use it. In descriptions of her garden, for example, the flora and fauna are sometimes described as moving to their own will, even if there's no breeze. Wild animals keep a wide berth of her land and garden. And her house doesn't necessarily always protect her from invasion. [SPOILER!!!!!!!!] In one of the Tiffany books Granny grudgingly approves of the cat You's mice catching abilities. So, Granny isn't necessarily able to keep them out of the house on their own (or doesn't want to use Borrowing to do it).
I always assumed that the reason the plans in Granny's garden moved by themselves was that they were magical plants anyway and that's why she grew them. Also that wild animals avoided the garden because those plants were predatory, and avoided the cottage because Granny is a witch. Though she had no trouble finding animals to Borrow.
Maybe the cottage itself allowed mice in so that You could catch them.