You replaced the flapper and the toilet is still running. Annoying — but good news: you’ve already ruled out the most common cause, and the remaining culprits are all under $20 and under 20 minutes. Here’s the exact order I check them in on a service call.
1. The chain is too tight (free fix, 30 seconds)
If the lift chain has no slack, the flapper never fully seats. Unclip it and re-attach with about a half-inch of slack — enough that the flapper drops flat but the handle still lifts it fully. While you’re there, make sure the chain isn’t getting trapped under the flapper edge.
2. The flapper doesn’t match the flush valve
“Universal” flappers aren’t. A 2-inch flapper on a 3-inch valve (common on post-2005 toilets) will leak from day one. Look at the drain opening in the bottom of the tank: baseball-sized = 2″, softball-sized = 3″. If you guessed wrong, see my tested picks by size in the Best Toilet Flapper Replacement guide.
3. The valve seat is pitted or crusted
Run a finger around the rim the flapper seals against. Mineral buildup or pitting breaks the seal no matter how new the flapper is. Scrub with a scouring pad (drain the tank first). If the seat itself is damaged, a seat repair kit with an epoxy ring beats replacing the whole flush valve.
4. The fill valve won’t shut off
Here’s the test that separates flapper problems from fill valve problems: put a few drops of food coloring in the tank. Color seeping into the bowl = seal problem (items 1–3). Water level slowly creeping up to the overflow tube instead = the fill valve is the culprit. They wear out in 5–7 years, sooner on hard water. The swap takes 15 minutes — picks and install walkthrough in the Best Toilet Fill Valve Replacement guide.
5. The float is set too high
If water spills into the overflow tube, the tank never stops calling for water. Adjust the float so the waterline sits about 1 inch below the top of the overflow tube. On float-cup valves it’s a screw or clip; on old ballcocks, gently bend the arm down.
6. The refill tube is jammed too far down
The little rubber tube clipped to the overflow should discharge above the waterline. If someone shoved it down inside the overflow tube, it siphons the tank continuously — a sneaky one that mimics a bad flapper.
7. A hairline crack in the overflow tube
Rare but real on older plastic flush valves. Water disappears below the waterline with no color-test evidence. This one means replacing the flush valve assembly — still DIY-able, budget an hour.
When to stop DIYing
If you’ve replaced the flapper AND the fill valve and it still runs, or the tank-to-bowl bolts weep when you work in the tank, call a pro before a $12 problem becomes a $200 floor repair.
Worn parts cause most of this. The two upgrades that end running toilets for a decade: a properly-sized flapper and a modern fill valve.
Fix the 12 Most Common Plumbing Problems Yourself — Free Plumber’s Handbook — including the toilet fixes plumbers charge $150+ for
Step-by-step fixes for the 12 most common problems — and exactly when to call a pro. Free and instant, from a licensed plumber. Save hundreds on calls you didn’t need.