Toilet is running but the flapper is clean and intact
There are a few places where the flap valve/overflow tube assembly could be leaking. Check for loose parts, but don't over-tighten or you'll crack plastic parts or, worse, the porcelain!




There are bolts holding the tank to the bowl, with rubber washers to prevent leakage. Make sure the bolts and nuts are tight -- sometimes, the tank will shift, loosening the bolts.
The flap valve seat (often part of the overflow tube assembly) also has a rubber washer underneath, and a foam rubber collar. If the valve seat is loose, the tank must be removed to tighten the large-diameter nut.
Check that the overflow tube is not cracked.
Check that the flap valve and seat are clean and have no splits or cracks.


See the City of Denver's tips on fixing leaks.