Lower Mills MWRA project: Workers unearthed a huge piece of ledge on Washington Street during the pipe replacement job last year. File photoArguing that they lost business when the Massachusetts Water Resources Authority replaced and rehabbed a major pipeline that ran through Lower Mills, a convenience store and a coffee shop on Washington Street are seeking a reimbursement from the agency.

Metamorphosis and Flat Black Coffee have sent letters to the MWRA saying they lost customers and revenue during last year’s construction and want to be made whole for the losses. In May, a third business, Milton Hill Sport and Spa, also applied for reimbursement, but that request was denied, according to an MWRA spokeswoman.

The agency allows businesses to apply for reimbursements by providing financial statements and tax returns that show a construction project’s effect on sales.

MWRA-hired contractors performed work on Washington Street between summer and fall in 2011. “During that period the section of Washington Street that we are located on was closed off or blocked off to traffic sometimes completely for a whole week Monday through Friday,” wrote Lefteris “Ted” Retzos, whose Retzos Brothers LLP owns Metamorphosis. “There was at times a small opening from River Street to Washington Street. However, for whatever reason, the Boston Police officers on duty for the construction were too restrictive in allowing the foot traffic to proceed.”

That resulted in business expenses exceeding their sales, he added. “An examination of our records shows our inability to generate personal income from the business and it is evidenced in the absence of payments to owners of the business.”

Flat Black Coffee, which owns another shop in the Ashmont neighborhood and a third outlet in downtown Boston, also said they lost business. “Due to the construction equipment, excavation, pedestrian and vehicle traffic re-routing and loss of on street parking we experienced a significant decrease in sales at this location,” wrote Jeffrey Chatlos, co-founder and co-owner of Flat Black. “Customers were either unable to access our store as normal, or only by spending an increased amount of time and with great difficulty.”

The Reporter obtained the letters through a Freedom of Information Act request submitted to the MWRA. The agency declined to release further documentation, saying the state public records law protects the confidentiality of financial information and tax return information, along with the agency’s own internal review process and analysis of the claims.

Businesses have a three-year window “from when they knew or should have known [their] business would be impacted” by the project, MWRA spokeswoman Ria Convery said.

Convery added that “each case is different and requires significant financial review, so it’s hard to say how long it will take.”

Chatlos, in a phone interview, said his business’s loss was “deep and hard felt.” He declined to provide a dollar figure, saying the loss was “substantial.” But he praised the agency as being helpful and cooperative and hoped for a resolution in a couple of weeks. “I have every confidence that they’ll do the right thing at this point,” he said.

The MWRA’s rehabilitation and replacement of the pipeline cost $14.5 million and disrupted traffic flow in Lower Mills for several months. But officials, who kept in close contact with Lower Mills business owners and residents, said the project was necessary because of the age of the pipe and a build-up of rust inside it. The line distributes water to Quincy, Milton, and the southeast corner of Boston.

In September, Milton Hill Sport and Spa owner Chris Orozzo said he had probably seen a 30 percent decline in business. “With so many detours, it’s not very accessible to our patrons,” he told the Reporter. “We’ve seen a decline in not only membership but also attendance to our facility.”