As far back as 2001, Turnpike Authority officials and contractors knew of thousands of leaks in ceiling and wall fissures, extensive water damage to steel supports and fireproofing systems, and overloaded drainage systems.[43] A $10 million contract, signed off as a cost overrun, was used to repair these leaks. Many of the leaks were a result of Modern Continental and other subcontractors failing to remove gravel and other debris before pouring concrete. This information was not made public; engineers at MIT (volunteer students and professors) performed several experiments and found serious problems with the tunnel.[44]
On September 15, 2004, a major leak in the Interstate 93 north tunnel forced the closure of the tunnel while repairs were conducted. This also forced the Turnpike Authority to release information regarding its non-disclosure of prior leaks. A follow-up reported on "extensive" leaks that were more severe than state authorities had previously acknowledged. The report went on to state that the $14.6 billion tunnel system was riddled with more than 400 leaks. A Boston Globe report, however, countered that by stating there were nearly 700 leaks in a single 1,000-foot (300 m) section of tunnel beneath South Station. Turnpike officials also stated that the number of leaks being investigated was down from 1,000 to 500.[44]
The problem of leaks is further aggravated by the fact that many of them involve corrosive salt water. This is caused by the proximity of Boston Harbor and the Atlantic Ocean, causing a mix of salt and fresh water leaks in the tunnel. The situation is made worse by road salt spread in the tunnel to melt ice during freezing weather, or brought in by vehicles passing through.[45] Salt water and salt spray are well-known issues that must be dealt with in any marine environment. It has been reported that "hundreds of thousands of gallons of salt water are pumped out monthly" in the Big Dig, and a map has been prepared showing "hot spots" where water leakage is especially serious.[46] Salt-accelerated corrosion has caused ceiling light fixtures to fail (see below), but can also cause rapid deterioration of embedded rebar and other structural steel reinforcements holding the tunnel walls and ceiling in place.[45]
The much larger than expected volume of water that must be continuously pumped consumes a correspondingly larger amount of electrical power, and will cause the pumps to wear out much sooner than originally estimated.