Soaring costs for the Steamship Authority’s expansive Woods Hole terminal reconstruction have reached new heights — just as construction reaches new depths — with the underwater portion of the project officially over budget after a frustrated board of governors reluctantly approved a $3.5 million change order at their meeting Tuesday.

The dockside rebuild, originally bid and contracted at $43.6 million with Jay Cashman Inc. of Quincy, has seen more than $13 million in change orders since it began nearly three years ago. And the marine construction phase continues to drag on, driving the price tag to about $56 million — about $3 million over original estimates.

Further cost overruns are expected.

Begun in 2018, the project to overhaul three ferry slips, transfer bridges and loading areas in the Woods Hole terminal will also experience significant delays, according to SSA senior managers, with construction now set to continue for an additional season.

“Obviously, we would want this to come in at or below budget,” SSA general manager Bob Davis said at the meeting. “But . . . going into the project there were a lot of unknowns. We didn’t know what was underneath the pier.”

Underwater obstructions in the Woods Hole harbor have flummoxed contractors since the project’s inception, with unforeseen rocks, boulders and other sea floor challenges accounting for most of the project’s change orders.

The latest $3.5 million change order comes after builders encountered a large boulder field in the vicinity of slip one, preventing Cashman from driving several monopiles to their designed depths.

Environmental engineers have redesigned portions of the project, including two monopiles, to avoid the construction obstacles, according to SSA managers, accounting for the added costs. But the $3.5 million does not include expected additional costs for a third monopile and changes to a stone groin.

The work will take place over a five-month period, from September through January 2022, with the added mobilization and demobilization periods also a factor in cost estimates.

“We had done sample drawings, but we couldn’t fill the entire site,” Mr. Davis said. “The time factor of this, it has now taken an additional season to accomplish. There’s a cost to that.”

The project is funded mainly through bonds issued by the Steamship Authority, as well as replacement funds generated by boat line operating revenue.

Initial marine-side cost estimates were developed by architects, consultants and in-house engineers, according to Mr. Davis, and included a five per cent contingency cost. Mr. Davis said the contingency should have been higher.

“Obviously in hindsight that contingency has been identified as a much larger percentage than what we had,” he said.

Meanwhile, early schematic designs for the landside portion of the project place cost estimates at approximately $31 million, according to a presentation Tuesday, including a permanent terminal building, expanded landscaping, bike parking and a dog park. The overall project cost is now pegged at more than $90 million.

The skyrocketing costs on the marine side rankled SSA governors.

“I’m definitely disturbed by this,” Falmouth governor Kathryn Wilson said at the meeting. “It appears as if the Steamship Authority is being taken advantage of.”

Mr. Davis said the change order initially was nearer $6 million, but that senior managers were able to negotiate it down to $3.5 million after evaluating the request from Cashman. He recommended approving the request, calling it a fair cost estimate — and noting that a rejection would lead to further delays, and higher long-term costs.

“Obviously, this is not something we take lightly, especially the scope of this change order,” Mr. Davis said. “We have been having multiple conversations with Cashman regarding this.”

Sensing that their hands were tied, unhappy governors voted 3-1 to approve the request and vowed to have better oversight on capital projects in the future. Ms. Wilson was the lone nay vote. New Bedford governor Moira Tierney, who has been a vocal critic of the change orders, was not in attendance.

“Let’s just move forward, lick our wounds, and get the job done,” Barnstable governor Bob Jones said.

“You’re damned if you do, and you’re damned if you don’t,” quipped Vineyard governor James Malkin. “And the cost of this is going to be borne by the people that travel to and from the Islands.”

In other business, governors approved an extension of reservation-only days on the Vineyard route until Columbus Day weekend, hoping to help alleviate traffic congestion concerns in Woods Hole.

Traditionally, the boat line operates on a reservation-only system during peak summer weekends between July 4 and Labor Day, with a dedicated standby for Islanders. But with traffic concerns piling up in Woods Hole, the reservation-only weekends will run for another month.

Governors also approved a slate of operational goals for Mr. Davis, including finishing the marine portion of the Woods Hole project by May 2022, and completing the design development phase of the Woods Hole terminal building. A final goal on the 12-point list calls for the general manager to develop a succession plan for his position.

Although June passenger traffic was down approximately 11 per cent over 2019, car traffic was up about two per cent from 2019, offsetting losses and putting the boat line in stable financial shape.

“Our fund balances are . . . in relatively good condition right now,” Mr. Davis said.