The Civil War forged the U.S. into a more centralized and nationalistic country, fueling a "full bore assault on tribal culture and institutions", and pressure for Native Americans to assimilate.

"[5] The United States Constitution mentions Native American tribes three times: These constitutional provisions, and subsequent interpretations by the Supreme Court (see below), are today often summarized in three principles of U.S. Indian law:[10][11][12] The Marshall Trilogy is a set of three Supreme Court decisions in the early nineteenth century affirming the legal and political standing of Indian nations.

Originally, the United States had recognized the Indian Tribes as independent nations, but after the Civil War, the U.S. suddenly changed its approach.

Thus, it required the federal government no longer interact with the various tribes through treaties, but rather through statutes: That hereafter no Indian nation or tribe within the territory of the United States shall be acknowledged or recognized as an independent nation, tribe, or power with whom the United States may contract by treaty: Provided, further, that nothing herein contained shall be construed to invalidate or impair the obligation of any treaty heretofore lawfully made and ratified with any such Indian nation or tribe.The 1871 Act also made it a federal crime to commit murder, manslaughter, rape, assault with intent to kill, arson, burglary, and larceny within any Territory of the United States.

The court provided a venue for prosecuting criminal charges but afforded no relief for tribes seeking to resolve civil matters.

In the interim, as a trustee charged with protecting their interests and property, the federal government was legally entrusted with ownership and administration of the assets, land, water, and treaty rights of the tribal nations.

In essence, the act broke up the land of most all tribes into modest parcels to be distributed to Indian families, and those remaining were auctioned off to white purchasers.

[21][22] Thus the Revenue Act declared that there were no longer any "Indians, not taxed" to be not counted for purposes of United States congressional apportionment.

A 1981 case, Montana v. United States, clarified that tribal nations possess inherent power over their internal affairs, and civil authority over non-members on fee-simple lands within its reservation when their "conduct threatens or has some direct effect on the political integrity, the economic security, or the health or welfare of the tribe."

Tribal sovereignty is dependent on, and subordinate to, only the federal government, not states, under Washington v. Confederated Tribes of Colville Indian Reservation (1980).

Where jurisdiction to try and punish an offender rests outside the tribe, tribal officers may exercise their power to detain and transport him to the proper authorities."

In response to this decision, Congress passed the 'Duro Fix', which recognizes the power of tribes to exercise criminal jurisdiction within their reservations over all Indians, including non-members.

In Iron Crow v. Oglala Sioux Tribe, the United States Supreme Court concluded that two Oglala Sioux defendants convicted of adultery under tribal laws, and another challenging a tax from the tribe, were not exempted from the tribal justice system because they had been granted U.S. citizenship.

The court cited case law from a pre-1924 case that said, "when Indians are prepared to exercise the privileges and bear the burdens of" sui iuris, i.e. of one's own right and not under the power of someone else, "the tribal relation may be dissolved and the national guardianship brought to an end, but it rests with Congress to determine when and how this shall be done, and whether the emancipation shall be complete or only partial" (U.S. v. Nice, 1916).

The court further determined, based on the earlier Lone Wolf v. Hitchcock case, that "It is thoroughly established that Congress has plenary authority over Indians."

Laws adopted by Native American governments must also pass the Secretarial Review of the Department of Interior through the Bureau of Indian Affairs.

With crime twice as high on Indian lands, federal funding of tribal courts has been criticized by the United States Commission on Civil Rights and the Government Accountability Office as inadequate to allow them to perform necessary judicial functions, such as hiring officials trained in law, and prosecuting cases neglected by the federal government.

The idea that tribes have an inherent right to govern themselves is at the foundation of their constitutional status – the power is not delegated by congressional acts.

As a result of a pair of treaties in 1830s, two tribal nations (the Cherokee and Choctaw) each have the right to send non-voting members to the United States House of Representatives (similar to a non-state U.S. territory or the federal district); the Choctaw have never exercised their right to do so since they were given the power and the Cherokee had not done so until appointing a delegate in 2019, though this delegate has not been accepted by Congress.

"[40] As determined in the Supreme Court case United States v. Nice (1916),[41] U.S. citizens are subject to all U.S. laws even if they also have tribal citizenship.

[42] The ruling's expansion of jurisdiction sovereignty also opened the possibility for Native Americans to obtain more power in alcohol regulation and casino gambling.

[47] Wartime industry of the early 1900s introduced uranium mining and the need for weapons testing sites, for which the U.S. federal government often selected former and current tribal territories in the southwestern deserts.

[48] Uranium mines were constructed upstream of Navajo and Hopi reservations in Arizona and Nevada, measurably contaminating Native American water supply through the 1940s and 1950s with lasting impacts to this day.

Under this model, the federal EPA sets water, air, and waste disposal standards, but delegates enforcement authority and the opportunity to design stricter environmental regulations to each state.

Enforcement authority over Native American territory, however, remains under federal EPA jurisdiction, unless a given tribe applies for and is granted Treatment as State (TAS) status.

[52] With the emergence of environmental justice movements in the United States through the 1990s, President Bill Clinton released executive orders 12898 (1994) and 13007 (1996).

[54] A recent challenge faced by Native Americans regarding land and natural resource sovereignty has been posed by the modern real estate market.

There is not regulation or legislation in place to sufficiently curb this practice at the rate necessary to preserve Native American land and natural resources.

[50] In 2023, the federally-recognized Resighini Rancheria of the Yurok People, Tolowa Dee-ni' Nation, and Cher-Ae Heights Indian Community of the Trinidad Rancheria announced that as territorial governments they have protected the Yurok-Tolowa-Dee-ni' Indigenous Marine Stewardship Area of 700 square miles (1,800 km2) of ocean waters and coastline reaching from Oregon to just south of Trinidad in the Redwood National and State Parks.