Harmful Algal Blooms and Hypoxia Amendments Act of 2008

Harmful Algal Blooms and Hypoxia Amendments Act of 2008 - Amends the Harmful Algal Bloom and Hypoxia Research and Control Act of 1998 to: (1) require the Secretary of Commerce, acting through the National Oceanic and Atmospheric Administration (NOAA), to establish criteria for determining which states should serve on the Inter-Agency Task Force on Harmful Algal Blooms and Hypoxia and to implement a nominations process to select representatives for such Task Force; and (2) require the Task Force's scientific assessments of hypoxia and harmful algal blooms (hypoxia) once (currently, every five years).

Requires: (1) the President, acting through the Task Force, to establish a national program to integrate efforts to address hypoxia research, monitoring, prediction, control, mitigation, prevention, and outreach; (2) the Task Force to be the oversight body for the development and implementation of the National Harmful Algal Bloom and Hypoxia Program; and (3) NOAA to be the lead federal agency for implementing and administering such Program. Sets forth the Program's responsibilities and duties, including: (1) promoting a national strategy to help communities understand, detect, predict, control, and mitigate freshwater and marine hypoxia events; (2) maintaining and enhancing the Ecology and Oceanography of Harmful Algal Blooms Program, the Monitoring and Event Response for Harmful Algal Blooms Program, the Northern Gulf of Mexico Ecosystems and Hypoxia Assessment Program, and the Coastal Hypoxia Research Program; and (3) establishing a Mitigation and Control of Harmful Algal Bloom Program.

Requires the national hypoxia program to: (1) oversee the development and implementation of Regional Research and Action Plans and identify regions and sub-regions to be addressed by each Plan; and (2) convene regional panels of experts. Requires each panel to develop a Plan that identifies appropriate elements for the region, including: (1) priorities for ecological and socioeconomic research on issues related to, and impacts of, hypoxia; and (2) state and local government actions that may be implemented to monitor, minimize, reduce, and address hypoxia.

Requires the Task Force to report to specified congressional committees not less than every five years on hypoxia.

Requires: (1) the Secretary, acting through NOAA, to establish a collaborative pilot program with the Environmental Protection Agency (EPA) and other federal agencies to examine hypoxia occurring in freshwater systems; and (2) such program to be located in the Mississippi River Basin watershed.