Initially, Theo's diary was a collection of his private thoughts, the kind of journal one would expect from someone who frankly describes himself as "a self-regarding and solitary man."
But over time, as Theo becomes more deeply involved with an antigovernmental group called The Five Fishes, he starts to realize that he's not just an isolated individual but part of something much bigger than himself. No longer characterized by what he calls "obsessive self-sufficiency," Theo is now dedicated to fighting for a noble cause that involves collective action.
One can see his throwing of his diary into a lake as a hugely symbolic act. In doing this, Theo is effectively rejecting his former self, the isolated, atomized individual who led a solitary existence. On a more mundane level, getting rid of the diary can also be seen as a necessary measure of self-protection. After all, the diary does contain a lot of incriminating information that could get Theo and the members of The Five Fishes into serious trouble with the authorities if they ever got their hands on it.
But it's the symbolism involved in Theo's throwing the diary into the lake that's important here. Theo's changed, and he's come to reject his former self—the self that is represented by the diary.