At the start of the map, take an immediate left at the intersection where the acid pool is located and shoot/hit the grate at the end of the path; there is a Green Armor inside.
Go into the room with the Gold Key door; there are Grunts and Ogres located inside, so be careful. As soon as you walk in, take a left and then another left around the giant yellow box to spot a grate on the wall; shoot/hit it to open it to get a large Box of Nails.
In the same room, you will notice a set of partially-opened doors that you cannot open. Right next to that, there is a staircase with a gap in the wooden paneling concealing a Shootable Button; shooting it will open the doors, leading to a path containing several large boxes of Nails and Shells, a Shambler, and a button that raises up one of the containers, revealing a Yellow Armor. CAUTION: Grabbing the Armor will raise the other container, which contains a Vore.
At the very bottom of the eponymous Wishing Well, there is a metal door that has been braced open by a crate; go inside to find a Floor Plate. Stepping on it displays the message "A door has been opened."; head around to the opposite side of this half of the room to find that the metal gate blocking the 100 Health has now been opened.
Inside the room past the Silver Key Door, there is a staircase on the far side (in between two giant boxes, one yellow and one red) leading down to a platform with a Vore, crates, acid and two tanks of some sort. Down here there are also two things that resemble generators, the sides of which contain 1 Button each; pressing both of them will open the wooden doors next to the staircase leading down here. Inside is a box that is being suspended in mid-air by a giant fan in the floor; jumping into the air stream will lift you up to 3 platforms in the room that cannot be reached otherwise (1 lower one in front of you and 2 higher ones on the left and right side). On the front platform there is a 25 Health, and on the upper platforms there is a Box of Cells and a Thunderbolt; grabbing the latter will cause the door where the Cells were located to open, containing a large Box of Nails as well as a large group of Scrags.