Ride the elevator up, right inside the entry. Run out on the bridge and dispose of the enemy there. Don't forget to bring your own can opener.
When you finish, go back to the elevator, jump down the hole and get off the lift, before it can get you up again. A door has opened in the wall, with some goodies inside.

Thanks to Mauritorami for this one!

Inside the first switch - operated door is a bridge. Opposite the bridge is a ledge with one or more zombies. Toss a grenade. The explosion opens a secret corridor to the ledge.

On the Zombie ledge, you can see a half-submerged door under the bridge. Secret inside. Go a bit fishing while you are down there anyway.

Grab the gold key, and get some Instant Company (TM)! Get rid of this annoyance, go inside the righthand alcove and shoot the back wall. Inside is a partially flooded room. Under the surface is a blocked door - that's the entry to the secret level "Underearth". You open this door in secret #4.

After avoiding the autoshooters, you are at a 'T' crossroads. The righhand corridor leads to the exit. Don't use the exit, or you will miss the secret level. Turn left, to the room with the button in the roof. Shoot it, and enter. When you press the wall switch inside, you enable acess to the secret level.

Facing the shooters again, to the left and right of the shooter corridor is ledges with goodies. The lefthand one is no problem, the righthand ledge is a tricky jump. Get over there, pick up the goodie.

A smaller ledge follows the wall - walk that way, enter the doorway, and jump down in the well at the end of the room - "The Well Of Wishes". Pick up the goodies and greet the dopefish (You'll find it in most ID games. It first showed in "Commander Keen 4"). Swim to the back corner of the submerged room. A door will open, right in front of the entrance to the secret level.