The storm flooded marshes, downed trees and changed shorelines in ways that could push birds to nest in other locations, give fish access to new areas and change the composition of forests.
"It's tremendously complex because all of the impacts work together," said Tim Dillingham, executive director of American Littoral Society, an environmental advocacy group in New Jersey. "Some of these we're not going to see the impacts of for a very long time."
Dillingham's group surveyed Sandy's impact on coastal habitats for the National Fish and Wildlife Foundation, which will use the information to help prioritize federal aid funding.
One focus is Great Gull Island at the eastern end of Long Island Sound. The storm shattered a dock, created breaches in two places and eroded beaches on the northern, southern and eastern sides. About 9,500 common terns and 3,000 roseate terns nest on the island each spring. The colony of roseates, which are listed federally as endangered, is the largest in the Western Hemisphere.
The storm dropped rocks and sand in some places while other parts of the island's shore were washed away or flattened, said Helen Hays, director of the Great Gull Island project, a tern-monitoring program of the American Museum of Natural History in Manhattan. "This is the most damage we've had in the period since I've been here," said Hays, director since 1969.
Common terns, which are listed as threatened in New York, prefer open, flat areas to build nests along low grasses and rocks. The roseate terns nest in spaces under rocks -- areas that may have filled with sand during the storm.
Hays said common terns should be able to find enough space to nest. The lack of a dock hampers rebuilding blinds and shelters for the roseate terns, a project that was to take place this year.
Scientists caution that habitat changes from Sandy aren't all potentially negative.
Sandy ruptured a berm and trail built across Sunken Meadow Creek in the 1950s. The structure had limited tidal flows to a salt marsh. Without the saltwater influx, invasive fresh water species pushed out native marsh plants. The berm also blocked saltwater fish such as alewife from using the creek to reach freshwater for spawning, said Ariana Newell, a natural resource biologist with the state Office of Parks, Recreation and Historic Preservation.
Alewife are "the living link that connects freshwater and coastal food webs," Maher said.
The parks department and Nature Conservancy had been working to remove the berm and install a bridge for people to use the area without restricting tidal flow. Sandy did part of the job for them.
Since then, tidal activity has increased in the marsh and some native species have returned, Maher said.
Sandy may also have made a positive impact in the Fire Island wilderness area, where a breach created by the storm remains open.
Jordan Rafael, a biologist with the Fire Island National Seashore, said it's too soon to tell what the long-term impacts from the breach and overwashes will be, but it could mean increased habitat for piping plovers and terns. Seals have appeared in the breach area.
"We're eager to see how wildlife will be utilizing the breach," Raphael said.
But on the North Fork, concerns have been raised by property owners planting small trees such as Bradford pear or kwanzan cherry to replace native oaks, sycamores and elms felled by Sandy, according to the Littoral Society report.
The tall native trees provide food and nesting places for owls, hawks and bald eagles that have been recolonizing around the North Fork. The non-native ornamentals will reduce the number of insects that feed on the trees and could reduce the number of birds, which feed on the insects.
"The replacement of natural forests and plants like invasives and exotic bushes, shrubs and trees is probably causing a silent ecological collapse of several of the ecosystems," Dillingham said. "Mother Nature has things in its place. Ornamentals really don't belong in the forest."