Right after you start the level, turn right. After a few houses you'll reach an entrance to an alley (where the Blue Key is located):

Inside this alley, there is a Shotgun Ammo in a bright wall patch:

Activate the region near the wall (not the wall itself) and an elevator will take you to the rooftop where the secret will register (containing an RPG and some Rocket Ammo):



Upon entering the Coffee Shop (using the Blue Key), to the right is the counter with the registers. The last one (with a keypad and button) can be activated (be sure to be looking at the button):


Doing it correctly will drop the bookcase across the room, below the "Pool Tables" (it closes fast so be sure to run to get inside). In there you'll find an Armor and a Night Vision Goggles:



As you exit the last secret, look to your right (towards the pool tables). You should spot an air vent at the end of the corridor:

Enter it and follow to get to another rooftop, with an Atomic Health for you:



In the trippy courtyard, there are two acid pools near a house:

Dive into the pools and in the middle there'll be an Atomic Health and a Devastator (between the two pools):

Next to the elevator that takes you to the Blue Key is a garage:

Go to the back end of the garage and look left where you'll see a grate with a side broken next to the garbage bin:

Enter it and you'll get the secret. Inside this bunker-like room you'll find an Armor and some Shotgun Shells:



Back to the street, follow it to the end (there's some kind of 24 hours store). Look up and at the top of the store there'll be a crack on the building wall:

Blow it up and you'll get a Holoduke:



Enter the market store. A bit forward to the right you'll see some carts:

Break everything in this vicinity (the carts, a broom, the glass and some jars with money). Jump into the hole behind the jars:

Inside you'll get an Armor:



Inside the bunker, right before the hole that goes to the cavern, to the left of the boxes are some bookcases:

Jump on top of the crates directly in front of the bookcases and they'll drop revealing a Scuba Gear:



As you enter the cave:

Dive underwater and be on the lookout to your right as you move forward to spot a small opening at the bottom:

Follow it to reach a cave where you'll find RPG Ammo and Devastator Ammo:

Right after the Red Key Door, turn left and go down the stairs:

Open the wall directly in front of the stairs to get the Shotgun Shells:



After the first secret, as soon as you come into the library turn right and navigate the bookcases to the end (where there's an Steroids on the floor):

The wall to the left at the end of the corridor can be opened revealing an Armor:



Right after the last secret, open the wall at the back of the secret room to reveal an Atomic Health:



From the last secrets, continue through the corridor, and go to the circular room in front of you in the back of the building. Turn around facing the entrance like this:

Jump on top of the first bookcase from the entrance, which will lower revealing an entrance with an elevator:

Ride the elevator to the top to get the secret and an Easter Egg:



After you blow up the wall in the bathroom:

Jump down the hole and, after you hit the water, swim up and look around to find a small room with some RPG Ammo:

When you reach the stairs leading to the temple:

Climb them and move to the left back towards the jeep and the Blue Key Device:

Jump on top of the temple nearby:

And climb to the top to get an Atomic Health:



Directly below the last secret is a small area with a Serious Sam Easter Egg. Approaching it (along with another Atomic Health) triggers the secret:



After dropping down inside the temple, as you climb the stairs, look to your right:

The wall ornament can be opened revealing a Pipe Bomb Crate:



Inside the entrance with the lava pool, one of the walls has a crack in it:

Blow both cracks (one behind the other) for an Armor and a shortcut out of the area:




Inside the entrance with the water pool (and some Octabrains), there'll be yet another crack on the wall:

Blowing up both cracks reveals a Medkit and a shortcut out of the area:




When you're aboard the spaceship, the area with the switch that exposes the generators contain the secret area:

In order to access it, make sure to destroy the generators:

After this, a section of the wall will become fake and you'll be able to pass through and see the Secret Exit Symbol:

After you leave the bathroom you begin in, turn right and enter the next bathroom area. To the right there'll be some lockers, and the leftmost one is larger than the others:

Open the locker and destroy the objects inside to reach an Atomic Health:



Leave the bathroom from the last secret and keep going to the right to the end of the corridor. There'll be lots of debris. You must shoot approximately where my crosshair is in order to trigger an explosion and clear some of the debris:

The explosion will reveal a small area with an Armor:



Enter the Battlelord arena through the door closest to the last secret. Moving to the right you should see a big hole on the ground:

Align yourself with the outer wall of the arena like my screenshot is and run towards the hole in order to fall on a small ledge in the middle of the drop:

This small ledge has an Atomic Health for you (here's an screenshot of me looking up from the ledge):



After you drop down the hole from the last secret, enter the corridor opposite from the Overlord and go to the left. At the end of the corridor you'll see a destroyed pillar and some water:

Jump on top of the pillar and a nearby wall will lower revealing some RPG and Devastator Ammo:



After you enter the Yellow Key Door:

Close it from the inside to spot a small hole:

Inside you'll find an Incinerator Ammo:

Right as you begin the level, turn right and move further into the office room. There's a chair here:

Destroy it to reveal a switch:

Activate it and turn around to see the secret area with a Holoduke:



As you leave the office room, some aliens open up apartment windows and start shooting at you from across the street:

Climb the nearby crate and jump into the lower window to get the secret and a little Easter Egg:



In the area where you obtain the Blue Key, there's an Alley Cat Lounge:

Inside, at the left corner, there's a "HOT HOT HOT" poster:

Activate it to reveal an RPG Ammo:



In the area where you obtain the Yellow Key, to the left there'll be a crack in the wall:

Blow it up to reveal a Medkit:



I highly recommend trying to get the Protective Boots before attempting this secret. I also haven't been able to return to the level without cheating so be careful when going for it.

In the area where you jump off the subway tracks onto some small pieces of land, look towards the farthest away acid waterfall:

Run and jump towards it: you'll actually start climbing it and reach a secret area with some Easter Eggs:

When you reach the USS Frisco:

Inside, at the back, there's a section of the wall that can be opened:

Inside, you'll find a Medkit (this secret is a reference to the Death Row secret in Episode 1):



When you climb the bridge after blowing up a section of it from inside the sub, turn right towards the beggining of the level, climb the bus and jump on top of the bridge support section:

Move around the right support and open the section perpendicular from where you jumped, revealing an RPG and some RPG Ammo:



After the boat ride, before entering the building, go to the other side and look up at the rock wall to spot a crack in the wall:

Blow it up to reveal a Chaingun and some Chaingun Ammo:



Right beside the Blue Key Door is a section of the wall that can be opened:

Open it to reveal a Medkit:



As you navigate the Fort, you'll reach a parking lot area. Directly across the bus, at the rock wall, you should spot another crack in the wall:

Blow it up to reveal a Shrinker/Expander Weapon and some Expander Ammo:

As you climb the mountain, right before the Battlelord, there'll be a crack in the wall:

Blow it up to reveal an Armor:



After defeating the Cycloid Emperor, look to the left to spot a crack in the wall:

Blow it up to reveal an Atomic Health:



After defeating the Overlord and entering the nearby door, look to the left to spot a switch on the back wall:

Activate it to reveal the secret containing some Shriker Ammo: