The phrase "bottom of the well" means being in a very difficult or desperate situation with no hope or way out. It refers to feeling trapped or at the lowest point of one's life. Full definition
Spirit Temple or Bottom of the Well before Deku Tree are my favorites from that particular game, and it leads to a lot of craziness I was hoping to see in BOTW. (gonintendo.com)
Once cool, carefully remove the cheesecakes from the pan (pressing up on the removable bottom of each well). (artofnaturalliving.com)
That bulk would make them behave a bit like heavy pebbles outpacing fine silt to the watery bottom of a well, jostling through the lighter surrounding stars to reach stable orbits very close to the Milky Way's core. (scientificamerican.com)