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Industry groups challenged a rule issued by the Army Corps of Engineers and the Environmental Protection Agency, designed to protect rivers, streams, wetlands and other waters from destructive discharges of dredged material. Earthjustice intervened to oppose the industry challenge. In February 2008, the dismissed the appeal by the industry groups.

Earthjustice intervened to oppose industry challenges to an EPA rule protecting rivers, streams and wetlands from oil spills.

The State of Hawai'i's Board of Agriculture approved a permit to allow the importation of algae that had never been introduced outside of the laboratory on the Kona coast of the Big Island. Earthjustice sued, and the Court has ordered that the Board's approval without a review of potential environmental impacts of the project was invalid.

Mountaintop removal coal mining, often described as "strip mining on steroids," is an extremely destructive form of mining that is devastating Appalachia. On behalf of local and national groups, Earthjustice is working in federal courts to bring the protections of the Clean Water Act to the people, communities and waters of Appalachia.

Earthjustice challenged permits granted by the Bush administration that approved the import of electricity generated at power plants in Mexico into the United States, even though the plants did not comply with relevant U.S. laws and regulations.

The Supreme Court in 2009 overturned a ruling by the Ninth Circuit Court of Appeals, allowing the destruction of a pristine Alaskan lake with toxic mine waste and setting a dangerous precedent.

Earthjustice successfully challenged the attempt by Kane County, Utah, to allow destructive off-road vehicles on federally protected lands.