Cheapest would be to take a bus from the Ashdod bus station to Jerusalem and then another bus from Jerusalem to Masada. For schedules and other information check www.egged.co.il/eng
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If you are coming off a cruise ship, bus to bus is the cheapest but it is also the least efficient and the one that will leave you the smallest amount of time at Masada~ I guess if that is ALL you want to do for one day, it is workable.
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