From the start point, go to the ledge overlooking the cavern. Below you (and to either side) is another ledge with some goodies.

Shoot the stained glass window. A small room to your left opens up, containing some armour.

In the room that leads to the underwater passage, there's a red button up high on the opposite wall. Takes some gymnastics to get to it, so just shoot it from below. This opens up a pair of rooms with a radiation suit to your left, and some ammo to the right.

It seems to count as two secrets - one as you enter each room. Blimey.

When you jump in the water, from the area in secret number 3, you'll see that one of the lights is flashing. Shoot the light - a wall underneath the water opens.

To the left, through the gold door, an ogre will come out of the wall. Just jump up where he comes from.