Dredges deepening the Savannah shipping channel last month killed two endangered Atlantic sturgeon and one green turtle, a threatened species. In addition, a maintenance dredge in the harbor killed a loggerhead sea turtle on New Year's Day.

The National Oceanic and Atmospheric Administration Fisheries Service, or NOAA Fisheries, sets limits on how many federally protected animals of each species can be disturbed or killed by these activities.

For Atlantic sturgeon in particular, the $706 million deepening project has already used up half its limit with two more years of dredging to go.

"It is concerning," said Bob Hoffman, protected species biologist for NOAA Fisheries. "And they get to get four. They've already started talking to us about this."

Atlantic sturgeon are long-lived, prehistoric-looking fish that can grow to 14 feet long. They spawn in rivers but spend most of their adult lives in estuaries and the ocean.

For green turtles, the NOAA limit is just three kills during the anticipated three years of dredging. Green turtles have a heart-shaped shell and grow to about 4 feet long. They were initially not expected to be encountered during the deepening project, but the U.S. Army Corps of Engineers a few years ago noticed warmer than expected waters into the winter dredging months. At the corps' request NOAA Fisheries in 2013 updated its incidental take levels to include green turtles. Maintenance dredging is subject to a separate set of limits that applies to all maintenance dredging projects from North Carolina to Port Everglades. It allows that dredging to kill 35 loggerheads, seven green turtles, seven Kemp's ridleys and two hawksbills annually.

For most of its dredging work, the corps employ hopper dredges, whose suction arms vacuum up silt and send it through giant rotating blades.

"Hopper dredges move relatively rapidly (compared to sea turtle swimming speeds) and can entrain and kill sea turtles as the drag arm of the moving dredge overtakes the slower moving sea turtle," federal biologists wrote in their biological opinion on the deepening project.

Dredging is limited to winter months to protect turtles, which are more abundant in the spring, summer and fall. Other precautions are taken, too. A trawler sails ahead of the dredge to clear the path of turtles, and each dredge's drag head is equipped with a cow catcher-like device meant to deflect turtles. A paid observer on board regularly checks for turtle remains in the screened overflow.

"Their job is to take it, determine what animal it was and report back," Hoffman said.

That's not always easy. Remains of a leatherback sea turtle's fore flipper were recovered during maintenance dredging in January.

"The specimen was fresh, but since leatherbacks are more apt to be in the water column than on the bottom of the river bed and are such powerful swimmers, it has been widely accepted that they are not taken by hopper dredges," corps spokesman Billy Birdwell wrote in an email. "Rather, carcass remains, usually as a result of large ship strikes, are recovered by hopper dredges after remains have settled to the bottom. Subsequently, this take was not counted against any allotted sea turtle take for the Savannah Harbor Expansion Project."

Scientists at the Georgia Department of Natural Resources reported that the remains appeared too decomposed for the turtle to have been killed by the dredge. They agree that the animal was struck by a vessel.

The dredging operation has also successfully relocated some animals captured in the deepening project, which will deepen the channel to 47 feet to allow larger container ships to ply the river more fully loaded.

"We have successfully caught and relocated two Atlantic sturgeon during SHEP dredging operations on Feb. 5 and Feb. 13, 2016," Birdwell wrote. In total, five sturgeons have been caught and relocated so far for the project, Hoffman said.

Federal guidelines allow up to 20 such relocations of these fish over the life of the project.

When dredging approaches or reaches any of the federal limits, NOAA Fisheries works with the corps to find ways to avoid harming the sea turtles or endangered fish. Options include changing the timing or location of the dredge.

Federal projects are rarely halted for surpassing the allowable "take" of endangered species, Hoffman said.

"It would be a rare, rare circumstance where a project would have to stop," he said.