Secretary of the Interior James G. Watt—already facing criticism related to his alleged hostility to environmentalism and his support of the development and use of federal lands by foresting, ranching, and other commercial interests, and for banning The Beach Boys from playing a 1983 Independence Day concert on the National Mall out of concerns of attracting "an undesirable element"—resigned abruptly after a September 21, 1983, speech in which he said about his staff: "I have a black, a woman, two Jews and a cripple. And we have talent. Within weeks of making this statement, Watt submitted his resignation letter.

Under the Administration of U.S. President George W. Bush, the Interior Department's maintenance backlog climbed from $5 billion to $8.7 billion, despite Bush's campaign pledges to eliminate it completely. Of the agency under Bush's leadership, Interior Department Inspector General Earl Devaney has cited a "culture of fear" and of "ethical failure." Devaney has also said, "Simply stated, short of a crime, anything goes at the highest levels of the Department of Interior.”

Gale Norton, Interior Secretary under George W. Bush from 2001–2006, resigned due to connections with the Jack Abramoff lobbying scandal. Julie A. MacDonald, deputy assistant secretary at the Interior Department appointed by Norton in 2002, also resigned after an internal review found that she had violated federal rules by giving government documents to lobbyists for industry.[5][6] On July 20, 2007, MacDonald's "inappropriate influence" led H. Dale Hall, director of the US Fish and Wildlife Service, to order a review of eight endangered species decisions in which the former deputy assistant secretary was involved. Hall has called MacDonald's disputed decisions "a blemish on the scientific integrity of the Fish and Wildlife Service and the Department of the Interior."[7] On 17 September 2008, the US Fish and Wildlife Service proposed to more than triple the habitat of the California red-legged frog, citing political manipulation by Julie MacDonald.[8] In a government report released in December 2008,[9] Inspector General Devaney called MacDonald's management "abrupt and abrasive, if not abusive,"[10] and U.S. Senator Ron Wyden, who commissioned the report, attributed the "untold waste of hundreds of thousands of taxpayers' dollars" to MacDonald's actions.[11]

On September 10, 2008, Inspector General Devaney found wrongdoing by a dozen current and former employees of the Bureau of Ocean Energy Management, Regulation and Enforcement, then known as the Minerals Management Service. In a cover memo, Devaney wrote “A culture of ethical failure” pervades the agency. According to the report, eight officials accepted gifts from energy companies whose value exceeded limits set by ethics rules — including golf, ski, and paintball outings; meals; drinks; and tickets to a Toby Keith concert, a Houston Texans football game, and a Colorado Rockies baseball game. The investigation also concluded that several of the officials “frequently consumed alcohol at industry functions, had used cocaine and marijuana, and had sexual relationships with oil and gas company representatives.” According to the New York Times, "The reports portray a dysfunctional organization that has been riddled with conflicts of interest, unprofessional behavior and a free-for-all atmosphere for much of the Bush administration’s watch."

On December 16, 2008, the Center for Biological Diversity sued the Interior Department under Kempthorne for introducing "regulations...that would eviscerate our nation’s most successful wildlife law by exempting thousands of federal activities, including those that generate greenhouse gases, from review under the Endangered Species Act." According to the CBD, Kempthorne's regulations violated the Endagered Species Act, "did not go through the required public review process" and "were rushed by the Bush administration through an abbreviated process" with "environmental impacts were analyzed in a short and cursory environmental assessment, rather than a fuller environmental impact statement."[23]