“The pizzas come out lighter and crispier and thinner,” said Mr. Lograsso, owner of Mamma Mia’s Trattoria & Brick Oven Pizzeria. Sales of pizzas have doubled since he adopted it, he says.

The new filters have also put Mr. Lograsso in hot water: A bagel shop in nearby Delray Beach claims it developed the technology to “Brooklynize” tap water, and an amended lawsuit filed in October in Florida’s Palm Beach County alleges the pizzeria has misappropriated trade secrets. The lawsuit was first reported in the Florida Sun Sentinel.

“There are certain things within New York City water that affect baking,” said Ira Marcus, an executive at the Original Brooklyn Water Bagel Co., who is also representing the company in the lawsuit. “We identified the key ingredients…through trial and error.”

Mr. Marcus contends the process was developed in 2007 by company insiders, including bagel-shop owner Steve Fassberg and his father-in-law, Donald Kurtzer. After a dispute, Mr. Kurtzer split off and formed Famous New York Baking Water Corp., which began marketing a system for replicating water.

The bagel company sued Mr. Kurtzer for misappropriation of trade secrets and the sides settled, but not before Mr. Kurtzer sold the only water-filtration system his company produced to Mamma Mia’s Trattoria in June.

The pizzeria denies accusations brought by the Original Brooklyn Water Bagel Co. and filed its own suit in federal court in September, alleging the bagel company has unlawfully claimed patents. “Basically anyone with a college chemistry background can figure out how to make it,” said John P. Kelly, the attorney for the pizzeria.

New York City water officials remain agnostic on the question of whether technology can replicate whatever is distinctive in the tap water. “We don’t know if it’s possible to truly replicate New York water but it’s not surprising that someone would try,” said Michael Saucier, spokesman for the Department of Environmental Protection.

The companies may be at odds over the water technology, but both think their facsimiles have surpassed the original.

“I was just in New York last weekend…I think mine’s better,” said Mr. Lograsso of his pizza.

“I think New York bagels are very good,” said Mr. Marcus. “Our bagels are better.”

Write to Maya Pope-Chappell at maya.pope-chappell@wsj.com