Clean Power Act of 2003 - Amends the Clean Air Act to require the Administrator of the Environmental Protection Agency (EPA) to promulgate regulations to achieve specified reductions in emissions of sulfur dioxide, nitrogen oxides, carbon dioxide, and mercury from certain electric generation facilities by January 1, 2009 (January 1, 2008, for mercury emissions). Directs the Administrator to establish an emission allowance tracking and transfer system. Makes a special rule for mercury emissions. Directs the Administrator to study the impact of emission allowance trading. Limits the trading of allowances with facilities other than electricity generating facilities to certain carbon dioxide emission control programs. Provides an allocation to: (1) dislocated workers; (2) disproportionately adversely impacted communities; (3) electricity generating facilities; (4) renewable electricity generating units; (5) efficiency projects; (6) cleaner energy sources; and (7) biological carbon sequestration activities. Directs the Administrator to establish and annually review emission limitations for mercury. Requires that captured or recovered emissions not be re-released into the environment. Requires the Administrator to request information from owners/operators about hazardous air pollutants other than mercury. Directs the Administrator to then propose and promulgate emission standards. Requires facilities to achieve specified emission standards should the regulations not be promulgated. Requires an assessment and identification of sensitive ecosystems and the objectives necessary for their protection, including the Adirondack, the mid-Appalachian, Rocky, and southern Blue Ridge Mountains. Includes as well the Great Lakes, Lake Champlain, Long Island Sound, and the Chesapeake Bay.