Maryland is turning to Florida as a source for the shells it needs to rebuild oyster habitats in Bay tributaries where oyster reefs have been degraded — or lost altogether.

The first shipment of 2,750 tons of ancient fossilized oyster shell arrived via train in mid-December from a Florida quarry where it is being mined. Another 112,500 tons of shell are expected to arrive over the next nine months.

Initially, the shells will help complete reef building in Harris Creek — the largest sanctuary-based oyster habitat restoration effort undertaken in the Bay. Later this year, they will be used to start a new project in the Little Choptank River.

The Maryland Department of Natural Resources is purchasing the shells for about $6.3 million from Gulf Coast Aggregates, near Carrabelle, FL. Under a deal arranged by the National Fish and Wildlife Foundation, CSX is hauling the shells from Florida to Baltimore at cost — something that saves $2.4 million, or about half of the transportation costs.

CSX will transport about 50 train cars of shell to Baltimore Harbor every 10 to 14 days through September 2014. There, the shells are loaded onto barges and hauled to restoration sites.

During a tour of Baltimore Harbor, where the first load of shells were being transferred from train cars to barges, Gov. Martin O’Malley praised the efforts of the foundation and CSX for making the project possible. “Through their generous contribution, we are moving our essential sanctuary work forward — work that is bringing our native oyster back to the Chesapeake Bay,” O’Malley said.

Michael Ward, CSX chairman and chief executive officer, said his company was “proud to be a part of this visionary public-private partnership to help restore one of our nation’s greatest natural assets, the Chesapeake Bay.”

Stephen Abel, executive director of the nonprofit Oyster Recovery Partnership said that as a result of the deal, more oyster shell will be placed in Maryland sanctuaries in the next nine months than in the last decade — enough to cover 80 football fields to a depth of 1 foot.

But the shells will actually cover a much greater area. To stretch the supply, DNR biologists will use rock and other substrate to build most of the 1-foot high reefs, then cover them with a thin layer of shell, said Mike Naylor, who heads DNR’s oyster restoration efforts.

State and federal agencies are working to restore 377 acres of oyster habitat in Harris Creek, a tributary of the Eastern Shore’s Choptank River. The project is expected to cost about $30 million over several years. It is, by far, the largest oyster restoration project undertaken in the Bay, but officials envision even larger ones in the future.

The draft of the new Chesapeake Bay Watershed Agreement calls for restoring oyster habitats and populations in 10 tributaries around the Bay by 2025.

Finding an adequate supply of oyster shell to make those projects a reality has been one of the most vexing problems for oyster restoration efforts in the Bay.

Oyster larvae, or spat, require a specific habitat. They need solid surfaces to land on — preferably oyster shell. But the amount of suitable surfaces in the Bay has been dramatically reduced in recent decades as oyster reefs have disappeared and hard surfaces have been silted over. Building new reefs requires putting hard substrate, such as rock or concrete, on the bottom, which is then usually covered with a layer of oyster shells.

The lack of habitat and loss of an adequate supply of shell are “major obstacles to all oyster restoration efforts,” according to a Chesapeake Bay oyster recovery plan released by the Army Corps of Engineers earlier this year.

Historically, shells came from oyster-shucking houses or from buried beds of fossil oysters under the Bay. But shucking houses don’t supply nearly enough shells to support the large-scale oyster restoration efforts envisioned for Harris Creek and other tributaries in coming years, and Maryland has difficulty attaining the permits necessary for dredging existing shell deposits from the Bay because of concerns about dredging impacts on other habitats.

It’s unclear whether the Florida quarry will be a long-term solution for restoration efforts. Oyster restoration efforts on the Gulf coast will soon be bolstered with recovery money from the Deepwater Horizon oil spill, and will compete for some shells, Naylor said.

“They may effectively outbid us, so this could be our last opportunity to purchase any shell,” he said. “We feel very fortunate to have had this opportunity, but it remains to be seen whether it is a long-term solution.”

As part of the Harris Creek project, Naylor said biologists are testing the performance of multiple substrates to help identify the best potential alternative for oyster shell.