Water can disappear from the bowl of the toilet through a crack in the toilet or through a crack in the pipes connecting to it. Check the surrounding area of the toilet for any leaks or drips.
Clean the inside of the bowl as grime build-up may obscure a crack in the porcelain. If no crack can be found, thoroughly checking the toilet bowl is necessary. Remove the toilet completely from the floor and manually pour water through the bowl to reveal the potential crack. If there is no crack, the vents that supply air for proper drainage are clogged or there is an issue with the sewer line and professional help must be reached.