Isn't that supposed to happen when you flush the toilet. You end up with waste water just sitting in the WC. If you don't want it there, just suck it out with a rubber hose.
The valve which lets the water in, however it works, has a rubber washer somewhere. There are many types these days so it's hard to say more. Also you may well have a valve which lets the water OUT of the cistern (instead of the older siphon) which will also have a rubber/plastic seal, which may be leaking.
In most cases the newer types have a push button to flush.
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