United States-Mexico Transboundary Aquifer Assessment Act - (Sec. 4) Directs the Secretary of the Interior, acting through the Director of the U.S. Geological Survey, to carry out a United States-Mexico transboundary aquifer assessment program to characterize, map, and model transboundary groundwater resources along the U.S.-Mexico border, in consultation and cooperation with the States of Arizona, California, New Mexico, and Texas (border States), the water resources research institutes (WRRIs) within the border States established under the Water Resources Research Act of 1984, Sandia National Laboratories, and other appropriate entities in the United States and Mexico.

Sets forth as the objectives of the program to: (1) develop and implement an integrated scientific approach to assess transboundary groundwater resources, including by prioritizing aquifers for further analysis; (2) expand existing agreements between the U.S. Geological Survey, the border States, the WRRIs, and appropriate authorities in the United States and Mexico to conduct joint scientific investigations, archive and share relevant data, and carry out any other activities consistent with the program; and (3) produce scientific products for each priority aquifer that are capable of being broadly distributed and that provide the scientific information needed by water managers and natural resource agencies on both sides of the border to effectively accomplish their missions.

Directs the Secretary to designate priority aquifers, including: (1) the Hueco Bolson and Mesilla aquifers underlying parts of Texas, New Mexico, and Mexico; and (2) the Santa Cruz River Valley aquifers underlying Arizona and Sonora, Mexico. . Directs the Secretary to work with appropriate Federal agencies and other organizations to develop partnerships with, and receive input from, relevant organizations in Mexico to carry out the program. Authorizes the Secretary to provide grants or enter into cooperative and other agreements with the WRRIs and other border State entities to carry out the program.

(Sec. 5) Directs the Secretary to coordinate the activities carried out under the program with: (1) the appropriate water resource agencies in the border States; (2) any affected Indian tribes; and (3) any other appropriate entities that are conducting monitoring and metering activity with respect to a priority aquifer. Prohibits the Secretary from initiating any new field studies or analyses under the program before consulting and coordinating with any border State water resource agencies with jurisdiction.

Requires the Secretary to work with appropriate border State water resource agencies, WRRIs, and other relevant entities to develop a study plan, timeline, and cost estimate for each priority aquifer to be studied. Directs that such study plan: (1) integrate existing data collection and analyses; (2) improve and strengthen existing groundwater flow models; and (3) be consistent with appropriate State guidelines and goals.

(Sec. 6) Declares that nothing in this Act affects: (1) the jurisdiction or responsibility of a border State to manage surface or groundwater resources in the State; or (2) the water rights of any person or entity using water from an aquifer.

(Sec. 7) Directs the Secretary, not later than five years after this Act's enactment and on completion of the program in FY 2014, to submit to the appropriate water resource agencies in the border States an interim and final report that describes activities carried out, conclusions relating to the status of aquifers, and participation of entities in Mexico.

(Sec. 8) Authorizes appropriations for FY 2005 through 2014. Directs that 50 percent of such amounts be made available to the WRRIs to provide funding to appropriate entities in the border States and Mexico to conduct activities under the program, including the binational collection and exchange of scientific data.
Output: A bill to authorize the Secretary of the Interior to cooperate with the States on the border with Mexico and other appropriate entities in conducting a hydrogeologic characterization, mapping, and modeling program for priority transboundary aquifers, and for other purposes.