Undulating meadows of seagrass beneath the Hudson River are key indicators of the waterway’s health — but the dense underwater fields have shrunk by more than 40% over the past two decades.

The New York State Department of Environmental Conservation has documented the sharp drop of seagrass, which scientists call submerged aquatic vegetation, since 1997. Similar surveys have found decreases in the Long Island Sound and along the Jersey Shore. The long tendrils of underwater greenery are a vital food source for birds and serve as protective cover for juvenile fish. Experts say human pollution and extreme weather are driving the seagrass’s decline, which threatens the fragile underwater ecosystem.

George Jackman, habitat restoration manager at the advocacy group Riverkeeper, likened the aquatic vegetation to a forest. “They’re equivalent to trees in a landscape, and when you have a forest, it becomes a refuge for a wide variety of creatures,” he said.

In the Hudson River, water celery and a variety of pondweed are the most commonly found submerged vegetation in shallower waters. The underwater fields of swaying tall grasses reach about 3 or 4 feet in height and are a nursery for many larval and juvenile fish, including alewife, perch and carp. The seagrass meadows provide minnows, shad and blueback herring with safe places to hide from predators.

“All these little fish need protection from big fish,” Jackman said. “There’s no free lunch in nature and predators are always on the prowl and prey species are always in danger of being eaten. They have to find cover and find protection.”

Some species, such as bay scallops, are closely tied to the survival of seagrass. But the once-abundant bivalves are hard to find in New Jersey’s Barnegat Bay and Long Island’s bays, according to Rutgers University ecology professor Richard Lathrop, who adds that submerged aquatic vegetation has also declined in these areas. Earlier this year, the New York Times reported on the dramatic decline of scallops off Long Island’s northeastern coast.

Waterfowl also use the grassy tendrils as a habitat and feeding ground. Ducks rely on water celery for food. Wading birds, such as snowy egrets and great blue herons, also feast on the aquatic vegetation at low tide.

“[Seagrass] creates diversity, niche space, and it allows for collections of species to thrive there collectively and provides refuge protection, oxygen, absorbs carbon dioxide, filters, sediments,” Jackman said. “You couldn’t have a more perfect machine and that’s what plants do: They provide the foundation for a lot of our ecosystems.”

Experts say increasingly frequent and strong storms are one cause of the decline in seagrass. Superstorm Sandy and Hurricane Ida, among other storms, increased the sediment and nutrients in the water, preventing light from reaching seagrass. Jackman said that after recent major storms, the Hudson River recorded significant decreases in submerged plants.

“When conditions are turbid, if there’s a lot of suspended sediment or if there’s a lot of floating phytoplankton [algae], that will cut down the light and stress the seagrass,” said Lathrop. “Seagrass do best when the waters are clear.”

In a healthy waterway, the submerged aquatic vegetation helps keep the water clear by filtering sediment through its roots and leaves.

Pollution is another reason seagrass is shrinking. In New York City, the combined sewer system discharges raw sewage into waterways during heavy rains. On Long Island, septic tanks leach sewage into the groundwater, which eventually ends up in the bay. Agricultural and lawn care runoff from fertilizers also add nitrogen to the water, encouraging the growth of algal blooms.

Carl LoBue, director of New York ocean programs for the nonprofit Nature Conservancy, said 70% of residents and businesses in Suffolk County aren’t connected to a sewer system. “They basically flush their toilets into the ground, and then that flows through the groundwater right into the bay untreated,” he said.

Boats are another problem, as their propellers can chop up the ribbonlike sea grasses, which can take several years to regrow.

“We’ve documented propeller scarring, boats basically driving over seagrass beds and ripping up seagrass,” Lathrop said. “That’s more of a spot disturbance, but we’ve mapped miles of propeller scars through the Barnegat Bay.”

Conservation efforts are in the early stages. One experimental method includes transplanting grass harvested from healthy waterways, though the strategy has had mixed results. The state Department of Environmental Conservation plans to begin rearing seagrass in greenhouses that will then be planted in the the Hudson River.

By the end of this year, the agency will release an updated map for the river’s submerged aquatic vegetation. It’s expected to reveal the extent of the underwater forest’s decline.

“Seagrass are really cool, just kind of swaying in the currents and just kind of floating over and seeing sponges and crabs, and some of the other critters that live there,” Lathrop said. “They really are an important part of our coastal system that may be somewhat underappreciated by the public. But they are a key component of our ecosystem, especially if you like to fish, you like to crab and [like] having healthy water quality.”