The U.S. National Marine Fisheries Service (NMFS) adopted a policy that would require fisheries scientists to count hatchery-bred salmon along with the population of wild salmon when making endangered species assessments.

Earthjustice sued on behalf of several conservation groups and groups of fishing enthusiasts, and on June 13, 2007, a federal court agreed that the policy was scientifically flawed and inconsistent with the Endangered Species Act.

Timber industry attorneys tried to force the U.S. Fish & Wildlife Service to remove the threatened marbeled murrelet from the Endangered Species Act. Earthjustice represented several conservation groups requesting "intevenor" status in the lawsuit.

On February 2008, a federal district court rejected the timber industry's suit. In a related matter a few weeks later, the FWS announced that it would not finalize a proposal that would have slashed murrelet habitat by almost 95 percent.

In July 2008, a federal judge in Washington, DC, and the Ninth Circuit Court of Appeals both ruled in favor of retaining federal Endangered Species Act protections for the marbled murrelet.

The genetic engineering of our agricultural products has created serious environmental problems and numerous questions about health and safety. The great majority of genetically engineered ("GE") crops are engineered to be resistant to a specific weed killer, glyphosate (known commercially as "Roundup," owned and marketed by Monsanto). These crops, known as "Roundup Ready," allow farmers to apply large quantities of glyphosate to their fields without harming the crop, but this practice accelerates the evolution of herbicide-resistant "superweeds." Farmers then apply greater and greater quantities of Roundup to try to kill these weeds, and when this fails, they use even more toxic herbicides. Also, the GE crops themselves can cross-pollinate or become mixed with other related crops nearby, contaminating their conventional or organic counterparts.

The U.S. Department of Agriculture, through its Animal and Plant Health Inspection Service, approved for commercial production genetically modified sugar beets without assessing the environmental, health, and economic impacts of these Roundup Ready beets, to the dismay of organic farmers, conservationists, and food-safety experts.

Earthjustice sued the USDA on behalf of organic seed producers and conservationists to get the deregulation of genetically-modified beets reversed until a full environmental impact statement is performed. In September 2009, the court agreed the USDA had violated the law and must prepare an EIS. Earthjustice is now seeking an injunction to stop further production of the sugar beets in the meantime.

The Fish and Wildlife Service approved several timber sales in areas nominally protected as critical habitat for the northern spotted owl. Earthjustice sued to stop the sales. In February 2007, the Ninth Circuit Court of appeals ruled that the FWS violated the Endangered Species Act when it approved the sales.

On October 17, 2006, the Environmental Protection Agency refused to strengthen the annual primary particulate matter standard, despite the nearly unanimous recommendation from its own Clean Air Science Advisory Committee that the standard be strengthened. In addition, EPA refused to adopt a more protective secondary standard to protect visibility, and revoked another annual standard for clean air. Earthjustice challenged this action, and in February 2009, a federal court ruled that these Bush-era clean air standards were deficient, and sent them back to EPA for corrective action.

Earthjustice is challenging the EPA's new source performance standards (NSPS) for steam generating units at coal-fired power plants and other industrial, commercial, and institutional facilities.  

In 2003, the Washington State legislature passed the Municipal Water Law, which promotes irresponsible development at the expense of junior water rights holders and stream flows for fish. The law redefined "municipal water supplier" to include any private developer with connections for 15 or more homes and allows these developers to benefit from expanded rights granted retroactively to municipalities. It carried out these changes without the state Department of Ecology's usual review of the impacts of the expansion of a water right. The law therefore violated the due process rights of water-rights holders. It also violated the separation of powers by retroactively overruling a decision of the Washington Supreme Court.

In June 2008, a judge ruled that the state legislature overreached by redefining developers as "municipal water suppliers."