TRANSPORTATION SECRETARY Stephanie Pollack announced on Thursday that she intends to replace the deteriorating, elevated portion of the Massachusetts Turnpike near Boston University with an at-grade highway and make room for the roadway by elevating Soldier’s Field Road above it. The highway arrangement, with commuter rail tracks alongside, is expected to allow enough room for separate bike and pedestrian paths along the Charles River.

Pollack has been struggling with the decision for months, and went back to the drawing board after her initial list of options were panned by transportation advocates. She brought in an independent review team, headed by Jack Wright of Weston & Sampson, the same engineer who figured out a way to build the Green Line extension for less, and his team proposed as an option the one she selected.

The secretary said none of the choices before her were perfect. Even the option she selected has weaknesses, she said. “It is very complicated to build and it will take longer and be disruptive to travelers,” she said in a telephone interview.

Her formal decision said the approach she selected would require the current bike/pedestrian path along the Charles to be closed for the entire eight-year construction period, so bikers would probably have to travel along the north side of the river.  Her option would also require the complicated relocation of water mains and utilities and the so-called Grand Junction Railroad that crosses the Charles and connects to Cambridge. Her formal decision said the Grand Junction, which is used by the MBTA to relocate equipment to the north side of the commuter rail system and by Amtrak and freight traffic, could be closed for four years “in the worst case.”

Despite the many negatives, Pollack said she concluded the approach she selected was superior to replacing the infrastructure as it is currently situated. “MassDOT should place more weight on the final condition of the infrastructure than on the construction-period duration and challenges. MassDOT will work to manage the construction period challenges as best as possible, but I believe the disruptions and costs of a longer and more impactful construction period are justified by the ultimate benefits.”

The other major option before Pollack was to put all the transportation infrastructure — commuter rail tracks, Grand Junction Railroad, Turnpike, Soldier’s Field Road, and bike/pedestrian path — at grade level. She rejected that approach because it would have required altering or filling a significant portion of the Charles River to make all the elements fit. She concluded the impact on the Charles, which she described as a protected resource under state and federal law, would not be allowed.

The cost of the construction project is currently estimated at just over $1 billion, but Pollack acknowledged cost estimates at this stage are iffy and could change. She said cost did not enter into her decision.

Pollack seemed pleased with the outcome. She said was proud the deliberative process was  transparent and she said it “identified a better way to build the project.”

A big hurdle that remains is when to build West Station, a new MBTA commuter rail and bus station to service the area. Pollack had originally proposed that construction of the station be put off until 2040, when Harvard University’s plans for the vast open space called Allston Landing become clearer. That timetable was met with fierce resistance by transportation advocates, who urged an earlier construction date.

Pollack said Thursday that she now plans to ask the team hired to design and build the new Turnpike when would be the first possible date West Station could be built, given that initial construction in the area will preclude starting the project. Once a date for possible construction is established, the secretary said, she will then begin a process to determine when the station should be built, taking into consideration service needs in the area.

Her formal decision said the project design must accommodate transit service leaving the future West Station and crossing the Charles River into Cambridge on the so-called Grand Junction Bridge. She indicated no decision has been made on whether that transit service will be rail or bus. Pollack also said she would like to see the bike path along the Charles connect over the new highway-train-Soldiers Field Road configuration to allow for north-south bike and pedestrian connections between the river and Commonwealth Avenue. The new bike bridge would require significant elevation — 30 to 35 feet on the north side, which is more than any other bike-pedestrian bridge in the city.

The state will now go through the environmental permitting process for the project, with the schedule calling for the filing of a final environment review by the end of this year. She hopes to start interviewing companies to design and build the project late in 2020, so the project is more than two years away from beginning.

The elevated Turnpike viaduct that runs between Boston University and the Charles River carries 150,000 vehicles a day and is the primary access point for vehicles coming from west of the city. The viaduct is structurally deficient, its supports are badly cracked, and the structure requires about $800,000 in annual repairs just to maintain it. Pollack said quick action is needed on the project to avoid the potential for weight restrictions that could dramatically affect vehicle travel in and out of the city from the west.