Paddle into the tunnel with the brick ledges on each side.
Head forward past these ledges and around the corner.
Continue forward under the falls into the low tunnel with the save/power-up crystal. This is SECRET #3. There are also some items on the ledges near the falls, which you'll get later on when you pass this way on foot.
Turn around and follow the tunnel back to the plug room.
Cross the pool and exit through the tunnel to the right of the raised alcove with the wooden door.
Paddle up the rapids...
...and around the bend to the left.
At the top is a calm pool with a crocodile swimming in it. Position the kayak near the middle of the pool and jump out (Roll + Left/Right). Then quickly climb out of the water on the stone ledge.
IMPORTANT: When you jump out of the kayak, be sure to do so in the middle of the little pool. The opening near the rapids is deadly. If you exit the kayak too close to it, Lara may die immediately, or you may find that you won't be able to get back into the kayak later.
Kill the poison-breathing lizard on the steps first.
Then take care of the croc.