Land that is privately owned will not be affected. The tribes often manage large amounts of reservation land in trusts, but fee simple/patent land (land privately owned outright) is protected by the constitutions of the states and federal government. Reservations are managed by the federal government via the Bureau of Indian Affairs. However, the tribes can establish many zoning rules, but they can be successfully challenged by private owners.

Here is a recent significant case about this matter where the courts sided with the non-Indian private land owner regarding a permit he received from the county even though he refused to also go through the Reservation's own permit process: https://caselaw.findlaw.com/us-9th-circuit/1651530.html