Clean Estuaries Act of 2010

Clean Estuaries Act of 2010 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to reauthorize the National Estuary Program.

Revises the purpose of management conferences convened with respect to estuaries. Requires a management conference's membership to include, among other entities, not-for-profit organizations.

Requires the Administrator of the Environmental Protection Agency (EPA) to: (1) evaluate, every five years, the implementation of each comprehensive conservation and management plan developed under the Program to determine the degree to which the goals of the plan have been met; (2) submit the results of the evaluation to the appropriate management conference for review and comment; and (3) report on the results of the evaluation and make such report available to the public in the Federal Register and on the Internet. Requires management conferences to update plans 18 months after they are evaluated.

Authorizes the Administrator to consider a management conference to be in probationary status if the conference has not received approval for an updated plan within three years of the date of the evaluation's publication. Requires the Administrator to: (1) reduce a grant for the implementation of a plan developed by a management conference with probationary status; and (2) terminate a management conference and cease funding for the implementation of the plan if the conference has been in probationary status for two consecutive years.

Requires, after the Administrator's approval of a plan for an estuary, any federal action or activity affecting such estuary to be conducted in a manner consistent with such plan. Makes EPA the lead coordinating agency for implementing plans.

Requires an agency head, in making annual budget requests, to consider the agency's responsibilities under the Program.

Repeals provisions authorizing the Administrator to give grants to individuals for the development and implementation of plans.

Authorizes appropriations for management conferences, grants, and monitoring the administration of plans.

Requires the Administrator to include measures to track the introduction and establishment of nonnative species within the trend assessment program that monitors variations in environmental parameters which may affect estuarine zones.

Requires the Administrator to evaluate and report to the public on the Program every five years.

Revises the definition of: (1) "estuary" to include near-coastal waters and other bodies of water within the Great Lakes similar in form and function to waters otherwise described in such definition; and (2) "estuarine zones" to include such waters and transitional areas, associated aquatic ecosystems, and those portions of tributaries.