Junction City in Kansas is facing that problem right now - about 30% of its water supply is missing. They are crediting the missing water to old and inaccurate water meters, water leakage and people stealing water from fire hydrants.
To fix this problem, the city is replacing the current meters and trying to more accurately account for water when flushing out fire hydrants. They are also finding more effective ways to meter water at wells and at water plants. The police department is encouraging the public to keep an eye out for people stealing water by filling up trucks or water trailers.