Middle Rio Grande Emergency Water Supply Stabilization Act of 2003

Middle Rio Grande Emergency Water Supply Stabilization Act of 2003 - Amends the Flood Control Act of 1948 to require the Secretary of the Interior to establish a program for financial and technical assistance to implement water conservation measures within the Rio Grande Basin in New Mexico, to be known as the Middle Rio Grande Water Supply Stabilization Program (the Program). Authorizes the Secretary to enter into cost sharing agreements with the State of New Mexico and other necessary entities to accomplish the goals of the Program.

Directs the Secretary to develop and implement a comprehensive and cost-effective program to identify, remove, and control phreatic vegetation in the floodplain of the Rio Grande River, and to replant and reestablish native vegetation as appropriate.

Authorizes the Secretary to establish a permanent conservation pool for storage of Rio Grande or San Juan-Chama water and to store water salvaged from water conservation measures for release to the Rio Grande River.

Directs the Secretary to provide direct financial assistance to the Indian Tribes and Pueblos to determine and quantify Indian water rights and water requirements and for conducting other water resource studies for the benefit of such Tribes and Pueblos.

Extends through FY 2008 basic research provisions and water desalination demonstration projects under the Water Desalination Act of 1996.