To fix a pop-up sink stopper, disassemble the stopper, inspect the rubber seal, replace the seal if necessary, and then clean the stopper. Reassemble the stopper before attempting to use the sink.
To disassemble the stopper, clean out the area under the sink, and then check to ensure that the pivot rod and clevis have a connection. Loosen the nut that holds the pivot rod, and then remove it from the sink. Mark the area where the clevis connects to the stopper rod, and then loosen the clevis screw. Soak all of these parts in vinegar or a cleaning solution.
Remove the stopper from the drain and look at the rubber seal at the bottom. If the seal looks weak or has cracks, replace it. If it's in good condition, reuse it, and just clean it with a brush, vinegar or cleaning solution before reassembling.
To reassemble the stopper, place it into the drain, and then place the clevis over the stopper rod. Put the pivot rod in the correct position, and then tighten the retaining nut to hold the pivot rod in place. Tighten the clevis screw at the mark, and test the stopper to ensure all parts work and move correctly. Lastly, tighten the retaining nut. At this point, the sink should hold water, and if it doesn't, adjust the nuts to ensure a good seal.