Coastal Zone Enhancement Reauthorization Act of 2003 - Amends the Coastal Zone Management Act of 1972 to authorize the Secretary of Commerce to make grants to any coastal State without an approved coastal zone management program if such State demonstrates that its grant will be used to develop a management program consistent with the Act's requirements.

Allows grants to States for administering a State's coastal zone management program to be used for developing and implementing coastal nonpoint pollution control program components.

Revises provisions respecting: (1) resource management improvement grants; (2) loan repayments; and (3) coastal zone enhancement grants.

Authorizes grants to coastal States to assist in specified community and local activities.

Authorizes the Secretary to conduct a cooperative program to develop and apply innovative coastal and estuarine environmental technology and methodology.

Changes from mandatory to discretionary the authority to conduct the "Walter B. Jones Awards" program to promote excellence in coastal zone management by identifying and acknowledging outstanding accomplishments in the field.

Revises National Estuarine Research Reserve System requirements.

Expresses the sense of Congress that the Undersecretary of Commerce for Oceans and Atmosphere should reevaluate shoreline mileage calculations used in the distribution of funding under the coastal zone management program to ensure equitable treatment of all regions, including Southeastern and Great Lakes States.