The pond has been running for a few days with no loss of water, so I'm proclaiming it fixed! In addition to fixing numerous leaks in the stream, I also had to rebuild the spillway for the waterfall. Somehow, the spillway rock got tilted backwards so the water was ending up in the ground. The pond liner under the waterfall should have collected the water and taken it back to the pond, but it, too, was tilted back. I guess we must have had some major ground movement back there.
The funny thing is that Jake pointed out the fact that the water was going backwards there. I should have listened to him earlier in the process, but the other problems needed fixed, too, so I guess it doesn't really matter.
Of course, since fixing the pond took so long, the weeds have once again taken over the yard. So much for being caught up.