Wells and springs should try to connect to aquifers (and vice versa)

When a Desert Well or Village Well generates, if there is an aquifer somewhere down below it within a minimum radius, then a water pipe should also generate and connect the two together. The water pipe can have twists and turns in it but it should be a continuous path of water source blocks going down to the aquifer.

Alternately, a new aquifer should generate at some random depth beneath any Desert Well, Village Well, or Village Spring. If the new aquifer connects to an existing cave network that is good for the player but it's not necessary. Enter at your own risk!

A third option would be to start with the aquifer. When an aquifer generates, there should be the possibility of a cobblestone well or spring to generate above it, at the surface. This can lead to wells and springs structures located in the middle of nowhere, far away from any village or other structure. But these would be possible entryways to water cave systems that don't require a player to go deep diving in the rivers.