"We want to protect our passengers from being annoyed," said Gisela Becker, spokeswoman for the city's transport authority HVV.
More than 500 security personnel will patrol the buses, trains and platforms checking for people drinking or carrying alcohol in open containers.
People caught will be asked to leave the train or bus and dispose of their drinks.
Becker stressed that the workers would be sensitive – there would be no searches. "Our men won't look deep into customers' pockets for the smallest drop of alcohol," said Becker.
But she added that personnel would be aware of people trying to disguise alcohol in soft drinks bottles. "Security will judge each situation individually and behave accordingly," she said.
Questions have been raised about how easy the ban will be to police, especially on football match days and at weekends near the city's famously licentious Reeperbahn. "That will be difficult," admitted Becker.
Christoph Kreienbaum, spokesman for Hamburger Hochbahn, the company that operates the network, told news magazine Der Spiegel, "In a carriage filled with fans, we won't try to impose the €40 fine on every single one."
They said the authorities would instead rely on passengers gradually getting used to the ban.
The Hamburg ban has re-energized a national movement to ban people from carrying open containers of alcohol in public, although this has failed many times before.
The German Association of Towns and Municipalities (DStGB) told the Passauer Neue Presse Thursday that Hamburg has set a "good example" that should be followed on city transportation systems throughout Germany.