Upper Colorado River and San Juan River Endangered Fish Recovery Act of 1998

Upper Colorado River and San Juan River Endangered Fish Recovery Act of 1998 - Limits to $100 million the costs of capital projects undertaken for the Upper Colorado and San Juan River recovery implementation programs (as agreed to in 1988).

Authorizes appropriations to the Secretary of the Interior, acting through the Bureau of Reclamation, to undertake capital projects under this Act. Terminates in 2005 and 2007, respectively, the authority of the Secretary to request appropriations to implement such projects for the recovery programs in the Upper Colorado and San Juan River basins. Authorizes the Secretary to: (1) enter into agreements for non-federal contributions to project costs; and (2) utilize for such projects power revenues collected pursuant to the Colorado River Storage Project Act. Limits such contributions with respect to each recovery program. Requires the Secretary to report to specified committees and subcommittees on the utilization of such power revenues.

Authorizes the retention of appropriated but unexpended project funds for use in future fiscal years.

States that nothing in this Act shall restrict the Secretary from funding activities or capital items in accordance with the Federal Government's Indian trust responsibility.