Immediately after the tunnel, you'll find a room where you can place the three Resonance Orbs.
Once you place the orbs, a passage will open in the wall above you. Take this corridor to enter The Deeplight.
Use Merryn to arrange the mirrors like the image below. Take the sub up.
Exit the sub and head to the right. Use Merryn to arrange the mirrors and prisms to only combine the red and green beams. Direct this new yellow beam into the sensor.
Before you leave, use the prism to direct the yellow beam at the wall blocking the treasure. Head down and use your knife to add the blue beam to the red and green to make white. White beams can destroy walls.
Collect your treasure, then point the beam at the mirror on the wall and the stone gate above. Do the same thing and you'll be rewarded with a Tyne Collector, upgrading your Tyne energy storage which lets you fire more torpedos before recharging at a Tyne Wellspring.
Head back to the sub and blow up the gate to the left.
Use Merryn to rearrange the beams again. First, create another yellow beam to gain access to the chest on the left and a treasure worth 75 coins.
Then create a purple beam and pass this and the green beams up to the sensors on the ceiling. Head back to the sub and continue up.
Head to the right to find the next Tyne Wellspring.
Use Merryn's knife to reflect the purple beam into the sensor on the right to turn the two gears on the right-hand side. Let them turn until they look like the image below.
Repeat the process on the left for the green beam.
Before you go, use your knife to reflect the green beam into the sensor all the way to the left. Let it rotate the mirror until it is horizontal. This will let you go claim the treasure for 50 coins.
Go back to the sub and head up. Exit the sub into the tunnel you see on your left.
Use the green blocks as shields and make your way down, left and back up. You'll pick up the silver treasure on the way. Head all the way around to the upper right corner to pick up a gem worth 100 coins, then go back to the sub.
Keep going up and to the right for the next Tyne Wellspring. Start the next puzzle by turning both double mirrors horizontally.
In the upper right, there's another double mirror. Turn it diagonally to let the blue beam pass. Only let it hit the sensor until the red beam strikes the sensor. Then hit it again to stop the mirrors from turning.
Move up a little and use your knife to reflect the blue beam into the combiner to make turquoise. Hold it here until the two mirrors are vertical and guide the blue beam into its sensor.
Head all the way to the left and use the knife to reflect the red and blue beams into their respective sensors until they align to direct the green beam into its sensor.
Take Merryn up along the path of the beam (not, mind you, The Path of the Beam, which is very different).
Hit the double-sided mirror directly along the beam first. This will activate a spinner that you will have to evade as you move around the room.
Work your way around the room clockwise, hiding behind any barrier you can and knocking off barnacles wherever you see them.
When you come back to the bottom, spin that first double mirror to reflect the beam to the right.
This will align everything so that the main white beam is heading up and out of this room and also breaking into red and blue beams being reflected back down and toward their sensors. Orient the mirror on the bottom left to bounce the red beam into the corner.
Head all the way back down on the left and back to the sub.
Take the sub up on the right hand side and out the top of that room.
Use the double mirror to destroy the wall to your right and break open the chest for a gold treasure.
Turn the mirror back to pass the beam up. Head left and destroy the gate above you, then head up to the next Tyne Wellspring.
Head to the right and use your knife to reflect the red, green and blue beams into their respective sensors to turn the gears and mirrors above the beam. The blue sensor turns the bottom row, the green sensor turns the middle two rows and the red sensor turns the top two. Work at it until they look like the image below.
After the cutscene, return to the sub and head up to the top to retrieve the Sonar Emitter.
Once Merryn installs the Emitter, use it to trigger the Sonic Switch to the right. This will also highlight the hidden passage to grab the coins and treasure below you.
Enter the current and let it push you all the way to the bottom of the tower. Stick to the left wall to grab a green gem right at the bottom.
Before you leave the tower, head up to immediately before the next room. Ping your sonar while between the two gold domes to reveal a hidden passage for Merryn.
Make your way past the spinning beams using the green blocks for cover to pick up a gold treasure worth 75 coins at the bottom. Make your way back to the sub.
Head all the way down. There's another sonic switch on the left that opens what looks to be an empty room. Ping your sonar to discover there's actually an invisible chest containing a silver treasure worth 50 coins.
Go back through the tunnel and exit The Deeplight. Right outside the tunnel, to the right of the diving bell you noticed on the way in, there's another invisible chest.
Keep heading right to the Tyne Wellspring and hermit crab.