Reconfirming long-held beliefs by local watchdogs and activists, the city comptroller’s office released a report recently saying that, from the beginning, the Croton Water Filtration Plant being built in Van Cortlandt Park has been, and continues to be, a huge, money-eating disaster.

Comptroller Bill Thompson’s office completed two separate audits on the project — one concerning the pace of the project and another concerning the cost of it.

“What we found was an embarrassment,” Thompson said, calling out the succession of commissioners at the Department of Environmental Protection (DEP) and Mayor Mike Bloomberg for their roles in mismanaging the project.

Thompson, a Democrat who is running for mayor, said the cost of the plant’s construction will exceed $2 billion, more than double the original estimate included in the DEP’s final Environmental Impact Staement (FEIS) of $992 million. If you include all the other costs associated with the project, the total price tag is nearly $3 billion. A review by the Independent Budget Office (IBO) in 2008 said the total price would exceed $3 billion.

When asked about some of the numbers included in the cost estimates, DEP officials simply could not explain how they came up with them, said Deputy Comptroller John Brown, who called the FEIS “deeply flawed.”

Brown said that when the Comptroller’s office first asked DEP officials about how they came up with the cost of the plant and why it’s so much higher than the estimate, they said the estimate was based on just 30 percent of the completed design, which is a low percentage, Brown added.

Then, when the auditors went back to them to say their explanation still didn’t make up for all the extra costs, the DEP responded by saying, actually, the estimate was based on just 10 percent of the design, Brown said.

Brown said there are still hundreds of millions of dollars in rising costs the DEP couldn’t explain.

Bronx Assemblyman Jeff Dinowitz, a longtime and vocal critic of the project, said the DEP deliberately “low-balled the estimate at Van Cortlandt Park” and inflated the cost of building it elsewhere in order to sell the project to the public.

“This is the biggest boondoggle in the history of New York City, and we’ve had plenty of boondoogles in New York City,” Dinowitz said.

The DEP has blamed the cost overruns on inflation and escalating construction costs. They’ve also said the original design estimates for the plant were conceptual so they could compare the costs of building at different sites.

But the DEP should have included inflation in its estimates, as well as a range of cost estimates based on design changes. Brown said all city projects normally include inflation and re-design cost estimates.

Thompson said the city might face up to $10 million in additional fines because the project won’t be completed by the federally-mandated deadline of October 2011. The audit said the project wouldn’t be completed until April 2012.

Thompson’s office offered 16 recommendations as to how the DEP could remedy the situation, including seeking a waiver for any potential penalties due to delays, immediately completing any outstanding designs and awarding contracts for remaining off-site work, incorporating a construction schedule to meet certain deadlines, and overseeing the work of consultants who do any future cost estimates.