Once you reach the "porch" of the green marble temple, find the only green torch. Press the use key on it to lower a lift on the opposite side of the porch. Ride it to the top, where a soul sphere is located.
After entering the temple, hug the left wall until you reach a security armor overlooking a bridge crossing some lava. The ground it rests on counts as a secret.
From secret 2, backtrack a bit and you will come across a stairway that dips down in the middle, with an opening to an outdoor area at the lowest point. Open the green marble wall across from the opening to find an ammo cache.
Halfway through the long red tunnel in the beginning of the level, there will be a niche to your right. Open the back wall to reveal a pair of medikits.
There is a S-shaped tunnel to the north-west from circular lava-filled room. After second turn, you can see a "vent" near the floor on the wall to your left. (Similar "vents" are commonly used in maps for setting off monsters by means of propagating player's gunshot sounds.) This "vent" is actually a fake wall, behind which lies the passage to a hidden room. Enter this passage and climb the stairs. As soon as you walk on the highest step, you will not be able to return the same way, being caught in an ambush. So stay on the second step from above and make an attack sound to attract the monsters. As they hear you, run down the stairs, wait at the passage entrance and enjoy the monster infighting. Dodge the projectiles that may be thrown at you. After some time, most monsters will have killed each other, so you will not lose much ammo and health. After killing everyone in there, flip the switch and step into the teleporter to be taken to the tunnel where you came from.
In the courtyard with tower in center, columns along the perimeter are placed in a pattern, alternating between stone and metallic. Metallic ones can be lowered to reveal some goodies. Look for the column that breaks the pattern (in the southwest corner), which contains a megasphere.