Through the darkness - the shaft going down in the big room with the 2 statues in it.
And because you can't see the way, you need a light first.
To get light, charge the crystal from the upper right chamber - in the room with the sunfish and the sun rays.
The crystal does always swim in it's little boat, which is unsinkable until you've charged it; but it can be bound and dragged around at the surface.
Use the gear (in said big room) to adjust the water level up and down to maneuver the crystal into that room.
After charging the crystal, bind it and drag it with you, into the darkness.
I could also hack together an overview pic real quick if you want...