Go inside the first door and shoot the two switches inside, under the roof. This solves a small problem a few yards further down, and yields a yellow armour.

In the waterfilled cave, a bit to the right and a few feet down, is a small hole. Goodies inside.

If you press the five floor switches in the Shooter room, two doors open. Drop down both of these, and press the wall switches. Don't forget the goodies. Quake tells you that "A secret cave has opened...." Finish the level, but don't exit - get back into the waterfilled cave.

A big hole has opened underwater, roughly opposite secret #2. Please enter, here is a slipgate to a secret level: Ziggurat Vertigo.