Harmful Algal Bloom and Hypoxia Amendments Act of 2004

Title I: Harmful Algal Bloom and Hypoxia Amendments Act of 2004 - Harmful Algal Bloom and Hypoxia Amendments Act of 2004 - (Sec. 102) Amends the Harmful Algal Bloom and Hypoxia Research and Control Act of 1998 to remove the President's authority to disestablish the Interagency Task Force on Harmful Algal Blooms and Hypoxia. Requires the Task Force, in developing its assessments, reports, and plans, to consult with the coastal States, Indian tribes, local governments, appropriate industries, academic institutions, and nongovernmental organizations with expertise in coastal zone science and management.

(Sec. 103) Directs the President, in consultation with the chief executive officers of the States and other specified entities, to develop and submit to Congress a report that describes and evaluates the effectiveness of measures that may be utilized to protect the environment and public health from the impacts of harmful algal blooms. Requires a period of public comment prior to submission of the report.

(Sec. 104) Requires the Secretary of Commerce (Secretary) to provide for local and regional scientific assessments of hypoxia and harmful algal blooms, as requested by States, Indian tribes, and local governments, or for affected areas as identified by the Secretary.

Directs the Task Force to complete and submit to Congress scientific assessments of: (1) current knowledge about harmful algal blooms in freshwater, including a research plan for coordinating Federal efforts to better understand freshwater algal blooms; (2) hypoxia in U.S. coastal waters including the Great Lakes; and (3) harmful algal blooms in U.S. coastal waters.

Requires the Task Force to develop and submit to Congress a plan providing for a comprehensive and coordinated national research program to develop and demonstrate prevention, control, and mitigation methods to reduce the impacts of harmful algal blooms on coastal ecosystems (including the Great Lakes), public health, and the economy.

(Sec. 105) Authorizes appropriations.

Title II: Miscellaneous - (Sec. 201) Authorizes the Secretary to make available to the University of Miami, by easement, lease, license, or long-term agreement, real property under the administrative jurisdiction of the National Oceanic and Atmospheric Administration (NOAA) on Virginia Key, Florida, for development by the University of a Marine Life Science Center.

Authorizes the use of such property by the University for the development and operation of facilities for multidisciplinary environmental and fisheries research, assessment, management, and educational activities, subject to agreement with the Secretary.

Authorizes the Secretary to enter into an agreement to occupy facilities constructed by the University on such property and to participate with the University in collaborative research at, or administered through, such facilities.

(Sec. 202) Authorizes the Secretary to convey to the Government of Mexico, without consideration, all right, title, and interest of the United States in and to the NOAA vessel WHITING: (1) for use as a hydrographic survey platform in support of activities of the U.S.-Mexico Charting Advisors Committee; and (2) to enhance coordination between the United States and Mexico regarding hydrographic surveying and nautical charting activities in the border waters of both countries in the Gulf of Mexico and the Pacific Ocean.