The Environmental Protection Agency rules set out schedules for how frequently airlines must flush and disinfect the water systems on planes and test for coliform bacteria.
Coliform are usually not harmful, but they are considered an indicator of the presence of disease-causing germs.
The schedules vary: Airlines that test water quality frequently don't have to disinfect and flush as often; those that test less often must disinfect and flush more frequently.
The rules apply only to tap water supplied through aircraft water systems, not bottled water.
The EPA determined five years ago that airlines weren't complying with drinking water regulations. The agency tested water from 327 planes, of which 15 percent tested positive for coliform. The agency said about 20 percent of the water tested didn't show any amount of chlorine - an indication it had not been treated.
Forty-five domestic airlines have already agreed to monitor their tap water quality and publicly report the results under a settlement with EPA.
The rule released Tuesday gives airlines up to 24 months before they have to comply with the new schedules.
The EPA estimates the cost of the new rules at nearly $7 million a year, or about a penny per ticket.
"This rule is a significant step forward in protecting people's health when they travel," said Peter Silva, assistant administrator for EPA's Office of Water. "EPA has taken this step to make sure the public has drinking water that meets standards, both in the air and on the ground."
Officials for the Air Transport Association, which represents major air carriers, had no immediate comment.