Water Rights Protection Act - Prohibits the Secretary of the Interior and the Secretary of Agriculture (USDA) from: (1) conditioning the issuance, renewal, amendment, or extension of any permit, approval, license, lease, allotment, easement, right-of-way, or other land use or occupancy agreement on the transfer or relinquishment of any water right directly to the United States, in whole or in part, granted under state law, by federal or state adjudication, decree, or other judgment, or pursuant to any interstate water compact and such Secretaries; and (2) requiring any water user to apply for a water right in the name of the United States under state law as a condition of such a land use or occupancy agreement.