Inside of the Jamaica Bay National Wildlife Refuge, a lone swan sits on the water, grooming itself. It is backed by the tall marsh grasses that characterize this swampy preserve, and behind those, I can see the Manhattan skyline.

The refuge, which encompasses 9,155 acres just east of Brooklyn and Queens, is such a haven for birds, from oystercatchers to willets and ospreys, that an estimated 20 percent of North America’s bird species visit it annually.

What makes the refuge more striking, though, is its proximity to one of the world most intensely urban areas. Less than an hour outside of Manhattan by subway, it sits just southeast of the runways at JFK, so that a visitor to the refuge hears not only a profusion of wild bird calls, but also the constant blast of man-made birds taking off nearby. When the twin towers fell in 2001, 29-year Park Service veteran Eduardo Castillo was watching from the shoreline of Jamaica Bay, just a short walk from his post at the refuge visitor’s center.

Along with such closeness to the city, however, comes exposure to a range of pollutants that threaten the health of the ecosystem. Four wastewater treatment plants discharge into the Bay, leading to elevated nitrogen levels that harm animal and plant species. Development in Brooklyn and Queens continues to reduce available habitat, and dredging and digging projects have altered water flows. The rate of salt marsh loss in the bay is estimated at 54 acres per year, and is accelerating.

The city Department of Environmental Protection (DEP) has created a Watershed Protection Plan for the Bay, and the first draft of the plan  contains scores of proposals intended to improve the bay’s water quality, restore its ecology, and control upstream pollution. However, an advisory committee appointed to oversee the plan has criticized it for lacking enough quantitative goals, timelines, or cost estimates. “You can say you’re going to restore some oyster beds,” said committee co-chair Brad Sewell, an attorney for NRDC, “but are you going to restore one oyster bed, or 100 oyster beds?”

Because members of the advisory committee consider elevated nitrogen levels in the Bay from wastewater discharge to be the most urgent threat facing it, they have called for the creation of a separate, accelerated plan to address that issue.  “The DEP has been out of compliance with water quality standards for many years because of those wastewater facilities,” said Sewell. His group, the NRDC, has organized a campaign to urge the DEP to adopt a nitrogen reduction plan.

As I wandered through the Jamaica Bay Refuge on a recent visit, I came across a turtle in the middle of the path, attempting to bury itself in the sand to protect its eggs from predators. It was a basic survival mechanism, meant to diffuse a threat that the turtle has faced for eons. The external forces currently affecting Jamaica Bay are of a different sort: only humans can change them.