(Measure passed House, amended, roll call #96 (254-154)) Garrison Diversion Unit Reformulation Act of 1986 - Authorizes the Secretary of the Interior to plan and construct a multi-purpose water resource development project in North Dakota providing for the irrigation of specified acreage, municipal, rural, and industrial water, fish and wildlife conservation and development, recreation, flood control and other purposes in accordance with Federal reclamation laws and the Garrison Diversion Unit Commission Final Report (dated December 20, 1984). Declares that nothing in this Act precludes North Dakota from seeking additional federally-assisted water resource development projects in the future. Declares that nothing in this Act shall be deemed to diminish the quantity of water from the Missouri River which North Dakota may beneficially use, pursuant to existing rights. Deauthorizes the Missouri-Souris Unit of the Pick-Sloan Missouri Basin Program. Makes exceptions to the Commission's final report regarding the supply work capacities of the James River Feeder Canal and the Sykeston Canal. Declares that any investment in features of the Garrison Diversion Unit that are no longer used to full capacity shall be nonreimbursable. Provides that the mitigation for fish and wildlife losses incurred as a result of project construction shall be on an acre-for-acre basis, based on ecological equivalency, concurrent with project construction. Sets forth exceptions to implementing the final report with respect to fish and wildlife conservation. Prohibits the Secretary from altering the status of Sheyenne Lake National Wildlife Refuge prior to the completion of Lonetree Dam and Reservoir. Declares that the mitigation and enhancement plan shall not be limited by cost constraints in the final report. Declares that credit toward mitigation recommended in the final report for reservoir sites is not authorized. Authorizes the Secretary to develop irrigation in specified project service areas. Prohibits the Secretary from obligating construction funds for such areas prior to September 30, 1990. Directs the Secretary to submit a comprehensive report to the Congress, not later than the end of FY 1988, on the effects on the James River in North Dakota and South Dakota of water resource development proposals recommended by the Garrison Diversion Unit Commission. Prohibits specified construction projects prior to the submission of such report. Prohibits the Secretary from obligating funds to construct irrigation facilities in specified project areas until contracts providing for appropriate repayment have been executed. Authorizes the Secretary to develop irrigation projects in specified service areas within the boundaries of the Fort Berthold and Standing Rock Indian Reservations. Prohibits the Secretary from permitting the use of project facilities for non-project drainage not included in project design or required for operations. Declares that municipal, rural, and industrial water systems constructed under this Act shall utilize power from the Pick-Sloan Missouri Basin Program. Provides that costs allocated to irrigation which are beyond the irrigator's ability to repay may be repaid from power revenues, except that repayment for the Garrison Diversion Unit may not exceed 40 years from the date of first delivery. Provides a ten-year period for payment of any rate increase resulting from the deauthorization of irrigation areas. Authorizes the Secretary to construct municipal, rural, and industrial water systems to serve areas throughout North Dakota in accordance with a cooperative agreement between the Secretary and the State. Directs the Secretary to construct, operate, and maintain a Sheyenne River water supply and release feature for the cities of Fargo and Grand Forks and surrounding communities. Directs the Secretary to construct, operate, and maintain such municipal, rural, and industrial water systems deemed necessary to meet the economic, public health and environmental needs of the Fort Berthold, Standing Rock, and Fort Totten Indian Reservations. Authorizes municipal, rural, and industrial water systems to deliver water into the Hudson Bay drainage only after the Secretary has determined that adequate treatment has been provided to meet the requirements of the Boundary Waters Treaty of 1909. Provides for the construction of the Sykeston Canal as a functional replacement for the Lonetree Dam and Reservoir, after a repayment contract has been executed. Declares that the Lonetree Dam and Reservoir shall remain an authorized feature of the Garrison Diversion Unit after specified conditions are met. Deauthorizes the Taayer Reservoir as part of the Garrison Diversion Unit. Directs the Secretary to acquire acreage in the Kraft and Pickell Slough area and to manage such area as part of the National Wildlife Refuge System. Authorizes the Secretary to charge a surplus crop production charge until the costs of irrigation facilities are repaid. Makes such charge inapplicable to the Oakes Test Area for research purposes. Authorizes appropriations. Directs the Secretary to make an annual contribution to a Wetlands Trust, limited to a specified amount, if such Trust is established in accordance with provisions under this Act. Requires soil surveys to include an investigation of soil characteristics which might result in toxic or hazardous irrigation return flows.