Older-type stoppers are moved up and down by a three-part linkage consisting of a lift rod, a metal strip with holes in it called a clevis, and the pivot rod, which supports the stopper or may be connected to it.
If this linkage comes loose the stopper won’t work properly.
If a pop-up stopper won’t seal, pull it out and check for debris. Some pop-ups lift out, some wind out, and others require you to pull out the pivot rod to which they’re attached.
Wash the stopper and check the rubber seal. If it’s dry or cracked, replace it.
Reinstall the stopper and check the seal. If it still isn’t working, and you have a lift-rod type, use pliers or fingers to loosen the grub screw attaching the lift rod and the clevis. Pull the rod up, push the stopper down and retighten the screw.
If the problem persists move the pivot rod to a different hole in the clevis. To do this, squeeze the spring clip on the clevis and slide the rod out. Move the clip and rod to the next hole.