How do I know when I've 100%'d the game?

@Devon Parsons answered quite correctly, but to make the answer more complete:

1. The pond is a very clever map of the whole island. All parts of the lake facе to the corresponding areas. The lake's water corresponds to island's shore; and the wet shore (rocks) near the lake correspond to island's water in-between shore (where tree houses and shipwreck is located); actually you can see the shipwreck in the lake as a piece of metal; also you can see a woman statue, which correspond to the statue on the mountain.
2. 11 big lanterns are the lasers. If a lantern lit - the laser is activated.
3. 6 fountains are the obelisks. If a fountain is high in the air - all puzzles on the obelisk have been solved.
4. The flowers are the audio-logs. White flowers are the usual ones, yellow - are the golden, which you can find underground when open the mountain secret door. If a flower blossoms - the log were found and activated.
5. 7 clams are the vaults with sheet of paper inside. If a clam is open - the vault was open.
6. Finally and most importantly for the completion: 14 triangular leaves are the small 3x3 puzzles scattered around the whole island. If a leaf is sunken and hardly visible - the puzzle was solved.
7. Unfortunately, the lake doesn't label "usual" puzzles, to be sure that you've done them all you need to go to menu/saved games and check the first number to be 523 (the second and third correspond to the puzzles on the obelisks and number of the obelisks, they must be +135 +6, but you can check all of them with the lake and the obelisks themselves). Some of those "usual" puzzles are tricky to find, but most of them you won't be able to avoid when you will hunt for the listed above lake-things, the rest easy-to-miss-puzzles are the ones, which allows to use various shortcuts and shortcuts (these shortcuts should be relatively obvious). Once you've done all of these you should have 523 puzzles count, but if you stack you can use this manual, for example.

Your save file will be labelled with 523, +135, +6.

The lake next to the city is an indicator of your progress in the game. After completing every possible action in the game, all the lanterns will be lit (each one corresponding to a laser, except for the flickering one held by the statue, which is always lit); all the white and yellow flowers will blossom (I believe they correspond to the audio logs); the 6 fountains will spray high into the air (each one corresponds to an obelisk) and the clams underwater will be open.

I am unsure exactly what the clams relate to.

An easier way is to go to the lake and see if the lamp has went out.

In my play, I solved everything except one last puzzle (so 522 +135 +6) and one last audio log (so one flower not blooming).

I first sought out the last puzzle and completed it, and went back to the lake and saw the lamp still flickering. Then I traced down the last audio log and played it for once. After returning to the lake, I found the lamp completely went out. The statue underneath it also changed to a new pose.

Therefore I conclude that the lamp is an indicator of 100% completion. It's arguably easier to check out than looking in the pause menu and counting every single flower in the lake.