The top-most turret in this room is being blocked by a breakable platform. Destroy it to access the secret on the right.
The turret's bullets cannot reach the wall on the left! Break the platforms blocking the bullets so you can access this room's secret.
To access the final secret, simply jump down through these platforms and move to the right. Make sure not to touch the crystal!

The first secret in the Factory is semi-hidden here. To access it, use your dashing ability to get to the hole in the bottom right.
In this room, the bottom-most turret is blocked from reaching the fragile blocks on the very right. Destroy the platforms that are in the bullet's path accordingly to access this secret.
The last secret is found by dashing in the gap at the bottom of the screen and just dropping down. Time your fall so you don't get shot by the turrets above.

The first secret is found behind a breakable wall to the left. Remember that once you return, the bat puzzle will be reset.
The second secret is also found behind another breakable wall.
The final secrets are found behind a breakable wall and a floor which breaks when you stand on it. Compared to the first two secrets in Egypt, the floor secret is very subtle and missable! This is also the only double secret in the game.

The first secret is to the top-right of this screen.
The second secret is found to the right of these precise jumps.
The final secret for the caves is very missable! Make sure to jump over the ship and head to the left to collect the final moneybag.

The first secret in Catacombs is found in this screen. The wall to the right is breakable.
The second secret in Catacombs is found behind yet another breakable wall.
The last secret is found at the top of this screen, with two moneybags, one placed on either side.

The first secret is at the top right of this screen. Below the concealed passage are some breakable platforms, so use your reverse gravity ability to break them. Ahead is a difficult puzzle containing a moneybag.
The second secret is found at the right of this screen. This is a tougher than normal blocked bullet puzzle. After you enter the secret through the broken wall, you must progress through a platforming screen. Completing this secret also awards you with the Captain Viridian achievement.
Lastly, you must go to the left of this screen to access the final Sewers secret.

The first secret is in this screen, to the bottom-ish right. Freeze the snakes to access it.
This is another blocked bullet secret. On the left are some breakable blocks. You must jump on the platform directly to the right of those blocks so the bullets can destroy them.
The final secret in this stage is to the left of this screen. Good luck with the bat obstacle!

The first secret is found behind a precise jump through spikes with slow fall.
The second secret is hidden away to the left of this screen. On the leftmost spike pit, there is a lone platform. Land on it to reveal a passage leading to the secret.

The first hidden room is found through a little hole in the bottom right, first freeze the turret and then make sure you switch to Double Jump and Dash to get into the hole. Remember that if you pause, you will have unlimited time to switch to these two abilities using the ability menu.
The second hidden room is found at the top of this wall jump section. Switch to Wall Jump and Dash to reach it.
The final secret of your 100% run is hidden away to the bottom left of the screen, where there are breakable platforms. Don't miss this, or all of your time will have been wasted!