This secret is strange: You won't get credit for it. This is a bug in Quake2. Go to the blue-key door. To the right of it, there is a shootable wall. Jump in and get the goods. Don't fall down the crack.

Go waste the two big guys / start the pump. One of the demolition charges makes a hole in the floor. I suggest you don't jump in, but kill everything down there. A bit of the wall seem to be out of alignment with the rest, shoot it, and you have opened the entrance to this secret.

Go back to secret #1, and jump to the floor below trough the gap. Shoot the grid to your right and grab the goodies - this ain't a secret, it just hurts to get later on... Don't jump down to the BFG, but walk the ledge to the left, over the green acid. You'll end at a secret. Use a invunerabillity to get out again, just paddle trough the acid (ouch!), or rocket jump back up on the ledge.
Don't forget to pick secret #2 up on your way to the blue key.

This may hurt. Dive in, swim to the back wall and get the secret. Don't get too deep, or you'll be sorry!