I have a really weird issue: my toilet is running water, but it's not in the tank. It seems like there's a neverending small flow of water entering the bowl of the toilet from the left side of the bowl. How can I stop this "leak?"
Plumbing – How to stop a running toilet
plumbingtoilet
Related Solutions
That tube is supposed to be attached (often with a metal clip) to the overflow tube.
It shouldn't just be inserted down into that larger diameter plastic tube (overflow tube), since as you've found, it will pop out again.
We had a similar problem with our Duravit toilet. We followed the instructions above, and after pulling out both the intake water controller portion, as well as the flush control, he didn't find any calcium build-up: just some rust stains. 
As a final check, my husband reached down into the toilet tank and felt something stuck in the bottom stopper valve. He felt what he thought was a broken piece of rubber, and after tugging on it with some force, he pulled the foreign object out in his hand from the access hole in the wall, and found a perfectly intact, but dead scorpion
]2 It must have died just that morning when the toilet started running. Luckily he wasn't stung.
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Best Answer
When you can avoid using the toilet for a bit, put a little food coloring in the tank. If the water in the bowl changes color after an hour or so, the flapper isn't sealing properly and should be replaced. If the water is still clear but you see a flow of water, the fill valve isn't fully closing and water is entering via the line attached to the overflow tube. Typically, if I go through the trouble of replacing either of these, I replace the entire innards of the toilet.