Harmful Algal Blooms and Hypoxia Research and Control Amendments Act of 2011

Harmful Algal Blooms and Hypoxia Research and Control Amendments Act of 2011 - Amends the Harmful Algal Bloom and Hypoxia Research and Control Act of 1998 to require the President, through the Committee on Environment and Natural Resources of the National Science and Technology Council, to establish an Inter-Agency Task Force on Harmful Algal Blooms and Hypoxia (Task Force).

Directs the Under Secretary of Commerce for Oceans and Atmosphere, through the Task Force, to: (1) establish and maintain a National Harmful Algal Bloom and Hypoxia Program to develop a national strategy to address marine and freshwater harmful algal bloom and hypoxia events; (2) promote activities and an action strategy to implement such Program; (3) oversee the development and review of regional research and action plans for addressing marine and freshwater harmful algal bloom and hypoxia events; (4) maintain a focus on technology research and development for each of the categories of marine harmful algal blooms, freshwater harmful algal blooms, and hypoxia in monitoring, predicting, preventing, controling, mitigating, and responding to events; (5) expand the existing electronic clearinghouse to provide information about such harmful algal blooms and hypoxia; and (6) develop a mechanism to provide a reliable and cost-effective supply of toxin standards for comparative research. Establishes the duties of the Secretary and the Administrator of the Environmental Protection Agency (EPA) under such Program.

Directs the Administrator, through the Mississippi River/Gulf of Mexico Watershed Nutrient Task Force, to submit an updated assessment and a revised action plan prior to the implementation of any plan developed under such Act.

Directs the Task Force to complete and submit to Congress and the President a plan for reducing, mitigating, and controlling hypoxia in the Chesapeake Bay.