Swim down and forward, away from the trapdoor toward the opposite (far left) corner of the underwater room.
There you'll find another lever. Pull this to open a door elsewhere.
(A brief cut scene shows this door opening.)
If Lara's air meter is less than half full, return to the open trapdoor for air. Otherwise, after pulling the lever, swim between the pillars on the left and then down into the long tunnel you came through before (as indicated by the arrows in the screenshot above).
Follow this tunnel forward and down. At the bottom on the left is the tunnel leading up to the pool. If you have only a little air remaining, go that way and surface to breathe. Otherwise continue straight ahead, following the tunnel as it slopes upward. . .
. . . and then turns to the left. Here it is lined with blue tiles.
Follow it to another pool and climb out on the far side. In the far right corner is the door you just opened using the lever. Inside is secret #2.
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