Harmful Algal Bloom and Hypoxia Research Amendments Act of 2003

Harmful Algal Bloom and Hypoxia Research Amendments Act of 2003 - Amends the Harmful Algal Bloom and Hypoxia Research and Control Act of 1998 (Harmful Algal Act) to repeal the President's authority to disestablish the Interagency Task Force (thus retaining it).

Requires the Task Force to: (1) work with the appropriate State, Indian tribe, and local governments to ensure that the assessment and research plans fulfill the requirements of the Harmful Algal Act; and (2) complete and submit to specified congressional committees not less than once every five years scientific assessments of harmful algal blooms and of hypoxia. Specifies amended assessment requirements.

Requires the Task Force to: (1) make a specified scientific assessment of freshwater algal blooms; and (2) develop and submit to specified congressional committees a research plan providing for a comprehensive and coordinated national research program to develop prevention, control, and mitigation methods to reduce the impacts of harmful algal blooms on coastal ecosystems, public health, and the economy. Specifies research program requirements.

Requires the Secretary of Commerce, in coordination with the Task Force and appropriate State, Indian tribe, and local governments, to provide for local and regional scientific assessments of hypoxia or harmful algal blooms, as requested by State, Indian tribe, and local governments. Specifies assessment requirements.