Spoiler Warning: This is a puzzle late in the game and I'll discuss the mechanics of the puzzle here.
I'm stuck on one puzzle in The Witness, in the sunken ship:
I am confused about how to handle the multiple different color/size hexagons. Usually different size hexagons represent different pitches of background sound effects- Large=Low, Medium=Mid, Small=High. I can't recall ever encountering different color hexagons that are also different sizes.
When I listen to the sounds in the background, I frequently hear water-drop like sound which repeats "Low-High-Mid" over and over. There is also a sound kind of like a harp strumming (that's the best description I can come up with) which has a very fast "High-Mid-Low" pattern, and there is a low horn sound which seems to just have one pitch but die off in volume.
I had thought each color would represent one sound, but no color has all three pitches. I've tried every variation I can think of to solve L-H-M or H-M-L, and solving it with the active line and the ghost line but I can't seem to solve it. I've even tried recording it and looking at the spectral image in Audacity but it's not helping me.
Here is my super high-tech analysis in Audacity:
Best Answer
In my opinion, this is by far the hardest puzzle on the island, and it's only one of two or three where I needed some help when I played the game. You already made it further than I did at the time. :)
There is a fairly thorough guide on Steam for this puzzle, however it's more like an analysis of the puzzle which spoils the puzzle completely. Instead, I'll try to present the solution in a series of hints (in spoilers), in case you want to figure out the latter parts for yourself. The final solution is at the bottom of the answer, of course.