How do I fix a leak between the toilet cistern and the pan?

Telling the doughnut washer from the flush valve backnut, taking a close-coupled cistern off without breaking anything, and rebuilding the joint so it seals with almost no force.

Difficulty: intermediate
Time: 1 hr 15 min
Read: 5 min
Safety: caution

Short answer

Water that appears on the floor only when you flush is the doughnut washer between cistern and pan. Water present without flushing is the fill valve or the flush valve backnut above it. To fix the doughnut, isolate and empty the cistern, undo the two close-coupled bolts, lift the cistern off, fit a new doughnut wide-face-up, and tighten the bolts alternately until it stops rocking.

Two completely separate seals sit within a few centimetres of each other at the base of a close-coupled cistern, and they are constantly confused. The flush valve's own backnut seals the valve into the cistern and leaks all the time. The doughnut washer seals the cistern's outlet into the pan and leaks only when water is passing through it — that is, when you flush. Knowing which is which halves the job. The exploded drawing shows both.

Safety

Vitreous china cracks under uneven or excessive load and the crack is often invisible until the toilet is used. Close-coupled bolts are tightened alternately in small increments until the doughnut is compressed and the cistern stops moving — never until they feel solid. A cracked pan or cistern is a replacement, not a repair.

What you'll need

A new doughnut washer to suit your cistern outlet
A new set of close-coupled bolts, washers and wing nuts
A sponge and a bowl
Water pump pliers and a screwdriver
Silicone grease
A helper for lifting the cistern

The close-coupled joint, exploded — doughnut washer and bolt stack

Step by step

Establish which seal is leaking.Dry the whole area, then wait without flushing for an hour. Water appearing with no flush is the fill valve, the supply connection, or the flush valve backnut inside the cistern — not the doughnut. Then flush and watch closely: water arriving at the pan shelf immediately on flushing is the doughnut.
Rule out condensation before you take anything apart.A cistern full of cold water in a warm humid bathroom sweats, and the water runs down the outside and pools at the base. Dry the outside of the cistern and watch: beads forming on the porcelain are condensation, and the fix is ventilation rather than a washer.
Isolate and empty the cistern.Close the isolating valve on the supply. Flush and hold the flush open to empty as much as possible, then sponge the remainder out into a bowl. A cistern with water in it is heavy and awkward and will empty itself down your arm as it tips.
Disconnect the supply.Undo the supply connection at the fill valve, with a cloth underneath. If it is a flexible connector, this is easy. If it is a rigid pipe, be careful not to strain it — you have to lift the cistern clear afterwards.
Undo the close-coupled bolts.They are two bolts passing down through the cistern base into slots in the pan shelf, with wing nuts underneath. Hold the bolt head inside the cistern with a screwdriver and undo the wing nut. Old ones corrode; a little penetrating oil and patience is better than force, and if one shears, the whole set gets replaced anyway.
Lift the cistern off, straight up.Get help. Lift vertically so the outlet clears the doughnut without dragging, and set the cistern down on a towel somewhere it cannot fall. If it is a wall-mounted close-coupled cistern there may also be wall fixings to release first.
Clean both faces properly.Scrape the old doughnut off the cistern outlet and out of the pan's flush inlet. Old rubber sticks and leaves a film. Clean both back to bare, dry china. This is where a rushed job leaks again.
Fit the new doughnut the right way up.It is tapered. The wide face goes up against the cistern outlet and the narrow face goes down into the pan inlet. Push it fully onto the cistern outlet so it is square. A smear of silicone grease on the outside helps it enter the pan inlet without rolling — do not use silicone sealant.
Rebuild the bolt stack in order.Bolt head inside the cistern with its rubber washer under it, through the cistern base, through the pan shelf, then a plain metal washer, then the wing nut. The rubber washer inside the cistern is what stops the bolt hole leaking, and it is routinely left out.
Lower the cistern squarely and tighten alternately.Set the cistern down so the outlet enters the pan inlet without catching. Then tighten the wing nuts alternately, a quarter turn at a time, keeping the cistern level. Stop as soon as the doughnut is visibly compressed and the cistern no longer rocks. That is far less force than instinct suggests.
Reconnect, refill and test through several flushes.Reconnect the supply, open the isolating valve slowly, and let the cistern fill. Dry the pan shelf and the floor completely. Then flush several times, watching the joint each time with a torch. A doughnut leak shows on the second or third flush if it shows at all.

Common mistakes

Tightening the close-coupled bolts to stop a leak — The doughnut seals by contact over a wide area, not by pressure. Over-tightening cracks the pan or the cistern and the crack is invisible until it is used.
Reusing the old doughnut washer — It has taken a permanent set in the shape of the joint it was first compressed into. It will not seal in a slightly different position.
Using silicone sealant on the doughnut — It does not need it, the sealant stops the rubber seating properly, and it makes the joint very difficult to open next time.
Lifting a full cistern — It is heavy, awkward and the water goes everywhere. Empty it first with a sponge.

If it doesn't work

Still leaking after a new doughnut

Cause: Bolts uneven, so the cistern is sitting skewed; or the doughnut rolled going in — Fix: Take it off and look at the doughnut — a rolled or pinched one is obvious. Refit squarely and tighten evenly.

Water weeps from around one of the bolts

Cause: Missing or perished rubber washer under the bolt head inside the cistern — Fix: Fit the correct rubber washer under the bolt head. This is not the doughnut's job and no amount of tightening will fix it.

Leak with no flushing at all, from the base of the cistern

Cause: The flush valve's own backnut inside the cistern — Fix: Isolate, empty, and tighten or reseal the flush valve backnut. On an old valve, replacing the whole flush valve is often quicker.

The pan shelf is wet but the joint looks dry

Cause: Condensation running down the outside of the cistern — Fix: Improve ventilation and heating in the room. Insulated cistern liners exist but ventilation is the real answer.

A bolt sheared while undoing it

Cause: Corrosion — Fix: Replace the whole close-coupled bolt set. They are sold as a kit and are cheap, and reusing corroded ones is how you get here again.