>>723920101
>>723920267
Windmill-powered water-pumps are a real thing.
Of course we never see the storage tank it's being pumped into or anything like that either, but it's not unreasonable at all for something like this to exist in the village.
Kakariko Village is at a relatively high altitude compared to the river, so it makes perfect sense that they would pump water up to the village. Assuming the well taps into the water table, having the windmill go into overdrive could, in theory, cause it to drain as it draws too much supply from the water table.