Montana Water Rights Protection Act This bill authorizes, ratifies, and confirms a specified water rights settlement entered into by the United States, Montana, and the Confederated Salish and Kootenai Tribes of the Flathead Reservation of Montana. Specified claims of the tribes against the United States are waived and released. The bill directs the Department of the Interior to allocate specified amounts of storage water in Hungry Horse Reservoir for use by the tribes. It also permits the tribes to carry out specified activities related to the Flathead Indian Irrigation Project, such as rehabilitating structures, upgrading irrigation facilities, and restoring streams that are affected by such project. In addition, the bill (1) establishes, for purposes of carrying out the bill, the Séli&#353-Qlispé Ksanka Settlement Trust Fund; (2) requires Interior to offer to negotiate with Montana for the transfer of specified parcels of state land; (3) requires the National Bison Range to be held in trust for the benefit of the tribes; and (4) requires Interior to make certain payments to Lake and Sanders Counties in Montana for the restoration of the National Bison Range.