How to Get Rid of the Sewage Smell When Flushing a Toilet

If you smell sewer smells when you flush your toilet, this could be coming from one of two places. The odor can come from the internal S-trap of the toilet if there isn't enough water to fill it during the flush. The reason for this could be an improperly adjusted flapper or obstructions in the siphon tube at the bottom of the tank or the inlet holes around the rim of the bowl. The smells could also be the result of a leaking wax ring under the toilet. If that's the cause, it will smell even when you're not flushing.

Toilet sewer smells can come from low water level or a leak.
  1. Remove the tank cover and observe the flapper while you flush the toilet. It should raise almost vertically while water is draining and fall down when the tank is empty. Adjust the chain if it doesn't rise all the way. The chain may be caught on an obstruction or it may be too short. It may also be waterlogged and dropping too soon. If so, replace it with a new chain.

  2. Watch the water drain if the flapper appears to be working correctly. If it drains slowly, there may be mineral deposit build-up in the siphon hole or in the inlet holes around the rim. Scrape around the inlet hole with a knife if you suspect there are deposits there.

  3. Clean deposits off the inlet holes in the bowl with a brush and toilet bowl cleaner. If you can't remove the stains, poke the end of a coat hanger into each hole to chip off the deposits and widen it. You can also clean the inlet holes by pouring 1 qt. muriatic acid down the overflow tube in the tank. The acid will dissolve the deposits without harming the toilet.

  4. Remove the toilet by unscrewing the bolts with a wrench. Lift it off the floor if you can smell sewer gas even when you aren't using the toilet. Scrape the old wax off the flange with a paint scraper and inspect it. If it's corroded or set incorrectly, it may be preventing the wax ring from sealing, and the imperfect seal is allowing gas to escape.

  5. Repair a corroded flange with a repair plate, available at hardware stores. If the flange is set more than 1/4 inch below floor level, raise it with a flange extender, which you can also buy at the hardware store. Fit a new wax ring on the flange and replace the toilet.


  • If you suspect a leak from the bottom of the toilet, fix it as soon as possible. Water may be leaking onto the floor below the toilet, and this can rot the subfloor.

About the Author

Chris Deziel has a bachelor's degree in physics and a master's degree in humanities. Besides having an abiding interest in popular science, Deziel has been active in the building and home design trades since 1975. As a landscape builder, he helped establish two gardening companies.