The owners of Coffee Fresco in Swansea have already tried putting up plastic eagles, but now say handing out water pistols is their only option.
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It means diners can now squirt any bird that lands on their table.
The unusual move comes after years of pigeon-related misery, with the birds attempting to scavenge food from under the noses of customers.
Manager Gary Mills said: "It's been a problem ever since the shop opened but every summer it gets worse and worse, more pigeons come.
Owner Gary Mills said giving customers water pistols had proved popular
A customer fires a water pistol at pigeons, which cafe owners say have turned into a real nuisance
Soaking pigeons is a novel approach to dealing with swarms gathering outside the business
"We have put signs up saying 'Do not feed the pigeons', we have tried plastic eagles to scare them away, all sorts of things but now we have just reverted to giving our customers water squirters."
He said the move has proved popular, and stressed that it causes no harm to the birds if they are squirted.
Gary said: "They think it's hilarious but it is a pain. As soon as the table is clear the pigeons attack the left overs. We are always on our toes to get the tables cleared as soon as possible."
Cafe bosses said pigeons have been a nuisance ever since the business opened in Swansea
Large numbers of birds are known to gather around the cafe scavenging for food
"It doesn't harm the pigeons, in fact they are so used to it they just fly away and come back two minutes later.
"What can the council do? They have put stuff to stop them perching on surfaces above the building but they can't stop them landing on walkways. I don't know what the solution is."
One regular customer said: "I think it's a great idea and it appears to be quite effective.
"The café has been absolutely besieged by the pigeons, they even land on the tables as you're siting there."
Water pistols have proved a hit with customers, says owner Gary Mills
Another added: "It works. I've used it lots of times and have hit quite a few. They don't like it but it doesn't hurt them; they just fly away for a bit. They always come back.
"They have got quite used to it by now and they only have to see you pick it up and they fly off."
Swansea City Council has introduced a ban on feeding pigeons and seagulls in the city centre.