It’s still half dark on an April morning when agents with shotguns clamber into a few scuffed dinghies and push off from Oregon’s East Sand Island into the Columbia River Estuary. The agents load their guns and look up, waiting for their targets to fly overhead.

The sun crests the horizon and the 25-hectare island comes alive as its 30,000 double-crested cormorants begin taking to the water to swim and dive for fish. Suddenly shots ring out, and dozens of lifeless black cormorant bodies plummet from the sky. The agents, from the U.S. Department of Agriculture’s Wildlife Services Program, have come a step closer to thinning the island’s cormorant population by nearly two thirds to protect fish stocks—just days after a federal court decided that the ongoing national cormorant-culling program was being improperly applied.

The U.S. District Court for the District of Columbia ruled that the program is based on a flawed and incomplete environmental assessment when it should be based on a thorough and scientifically backed report. And court records show that in a number of other cases over the past 10 years federal judges have admonished U.S. wildlife agencies—namely Wildlife Services (WS), run by the USDA’s Animal and Plant Health Inspection Service, and the U.S. Fish and Wildlife Service (FWS)—over what some see as scientific missteps and bureaucratic inefficiencies in predator management programs.

In another case decided in April the U.S. District Court for the District for Montana rebuked the FWS for apparently bowing to political pressure and ignoring climate change science when it withdrew its proposal to list wolverines as threatened under the Endangered Species Act in 2014. Similarly, WS was chastised by the U.S. District Court for Western Washington (State) last year for failing to perform a thorough type of environmental study before proposing an increase in wolf culling there. And final decisions are now pending on two other WS cases questioning the research on which the service’s predator culling programs are based. Pamela Boehland, public affairs specialist for WS, declined to comment on these cases.

A Double-crested Cormorant.

BSIP/UIG via Getty Images

The USDA established Wildlife Services—then called “Animal Damage Control”—in 1895 to help farmers cope with rodents and predators that threatened their livelihoods. Today WS does that and more, from preventing bird–plane strikes at airports to minimizing property damage caused by species such as white-tailed deer and Canada geese. Agents often use traps, poison and guns. As development pushes humans and wild animals into closer contact, the program’s activities continue to expand, often putting it at odds with conservationists. “These cases and court decisions are unfortunately a regular feature of the legal landscape,” says Drew Caputo, vice president of litigation for lands, wildlife and oceans at environmental law firm Earthjustice. “While wildlife agencies typically do the right thing, they sometimes bow to political pressure and fail in their duty to protect wildlife.” Environmental advocacy groups including Earthjustice routinely sue wildlife management agencies, arguing that some of their management practices—including the cormorant cull—are not adequately grounded in current science.

Many in the aquaculture industry see cormorants as a threat to native fish stocks, especially salmon and steelhead trout in the Columbia River Basin near East Sand Island. The National Oceanic and Atmospheric Administration says cormorants in the area consume about 11 million baby salmon and steelhead per year—causing what the U.S. Army Corps of Engineers estimates as a loss of $2.6 million to the $50-million Columbia River fishery. “It’s a conundrum when you think about it, killing one native species to help others…but today it’s become necessary to do so,” says Blaine Parker, avian predation coordinator for Columbia River Inter-Tribal Fish Commission, which represents four Native American tribes with fishing rights along the river. “Since the 1990s avian predation has become a major stressor on these fish, which also face aquatic habitat loss, hydroelectric dams and declining water quality.”

In 1998 and 2003 the FWS issued two cormorant “depredation” orders allowing aquaculture industry members and state wildlife officials to cull 160,000 cormorants across the nation each year in the name of safeguarding fish stocks. The service has repeatedly renewed the orders. Under the National Environmental Policy Act (NEPA) all federal agencies must carry out analyses when proposing actions that might affect wildlife or the environment. Such analyses may be brief overviews called environmental assessments (EAs) for tightly focused issues or thorough reviews called environmental impact statements (EISs), required for complex decisions that would significantly affect the environment. Both EAs and EISs must state several alternatives to any proposed action and are reviewed by service decision-makers and the public. EAs require far less time, money and staffing.

The FWS’s two cormorant depredation orders went up for review in 2014 and the service conducted an EA, which concluded that extending the orders until 2019 would have “no significant impact” on the birds’ populations. Public Employees for Environmental Responsibility (PEER), an environmental advocacy group, saw this as a federal entity taking the easy road in making a decision that actually warranted an EIS. PEER sued the FWS in the U.S. District Court for the District of Columbia, which found glaring issues with the FWS’s 2014 EA: It said that the service recycled data instead of analyzing the latest scientific research, did not seek alternatives to culling and failed to take a “hard look” at its proposed actions—all in violation of NEPA. The court stopped short of determining whether or not the FWS should have completed an EIS because it said the errors in the service’s assessment made it unclear whether or not the orders would have a significant effect on the environment.

Before the court closes the case it has called for an additional briefing from the FWS on an appropriate “remediation plan,” including a possible end to the service’s mass cormorant culls. As the FWS comes up with such a plan—which will need to be reviewed in court once complete—the service’s two orders still stand, allowing the killing to continue.

The FWS acknowledged in its 2014 EA that it was “unable to complete a full analysis” of proposals for alternative actions and updates to its previous EA “[d]ue to resource limitations.” When asked via e-mail if the FWS believes it adequately assessed its cormorant culling program when it went up for review in 2014, Gavin Shire, the service’s chief of public affairs, told Scientific American he would not directly comment on the case because litigation is ongoing. However, Shire says, “[the FWS’s] wildlife management decisions are based on the best available science. We make every effort to ensure that we have the most up-to-date information and use the public comment period as a means to solicit it from all potential sources.”

Although many who work in certain industries—such as farming, housing and energy development—may believe they benefit from having fewer predators around, the environment as a whole can suffer. For instance, studies on wolf removal in Yellowstone National Park emphasize the importance of predators: Kill them off, and like a house with no foundation whole ecosystems can begin to collapse. “The predator-removal mind-set is deeply ingrained in many people, including those at these agencies,” says Bethany Cotton, attorney and wildlife program director at WildEarth Guardians, another advocacy group that challenges federal wildlife agencies over alleged lapses. “It’s based in deep-seated cultural myth, hatred and a lack of grounding in ecology and the natural sciences.”

Even some depredation supporters say federal entities sometimes miss the mark when it comes to wildlife management, as they attempt to appease those on all sides of an issue. “Political sway is a big problem for wildlife agencies,” says Lance Fisher, a professional fisherman and fishing guide based in Portland, Ore. “You would find better ecological balance if the experts at these agencies were left alone to do their jobs, but that’s not how it goes down.”

And not all those who farm or fish say depredation is necessary to safeguard their livelihoods. Some accept a certain amount of loss to predators as part of doing business, and find ways to manage. “We don’t let the predators live here, they let us live on their land,” says Trina Smith, guest services supervisor at B Bar Ranch, a “predator-friendly” Montana cattle operation that borders Yellowstone National Park. “We’ve had success and minimal loss to bears, mountain lions, wolves and coyotes because we raise horned cattle that can defend themselves against predators, keep our cattle in tight herds and do not bring calves—which tend to attract predators—into the basin.”

The White House’s Council on Environmental Quality (CEQ), established under NEPA in 1969 to coordinate federal environmental efforts, is supposed to minimize lapses in federal environmental policies. The council has laid out standards, to which agencies can be held accountable, for writing EAs and EISs. This includes when agencies must perform an in-depth EIS rather than an EA. “It is important to hold firm to the criteria that the Council on Environmental Quality has established for determining when an action ‘significantly affects’ the environment and therefore requires an EIS,” says Laura Dumais, an attorney at PEER who worked on the cormorant case. “Otherwise agencies will choose the easier EA route whenever they can.”