Clean Estuaries Act of 2011

Requires a management conference, in updating or developing a new plan, to make use of collaborative processes to: (1) ensure equitable inclusion of affected interests and the accessibility of relevant information to members; (2) engage with members of the conference through the use of consensus-based decision rules and assistance from impartial facilitators; (3) promote accountability and transparency by ensuring members are informed of conference purposes and objectives and evaluation results in a timely manner; (4) identify roles and responsibilities of members in conference proceedings and plan implementation; and (5) seek resolution of conflicts or disputes.

Considers a plan to be approved if the Administrator of the Environmental Protection Agency (EPA) fails to respond to its submission within 120 days. Requires the Administrator to terminate a management conference if it fails to submit or secure approval for a comprehensive conservation and management plan within three years of being convened.

Requires the Administrator to: (1) evaluate 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 every five years; (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 five 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. Requires the Secretary of the Army, the Administrator of the National Oceanic and Atmospheric Administration (NOAA), the Director of the United States Fish and Wildlife Service, the Secretary of the Department of Agriculture, the Director of the United States Geological Survey (USGS), the Secretary of the Department of Transportation, the Secretary of Housing and Urban Development (HUD), and the heads of other appropriate federal agencies to: (1) cooperate and coordinate activities, including monitoring activities, related to the implementation of such plans; and (2) collaborate on the development of tools and methodologies for monitoring the ecological health and water quality conditions of estuaries covered by a management conference. Requires EPA to serve as the lead coordinating agency for such activities.

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 FY2012-FY2017 for management conferences, grants, and monitoring the administration of plans.

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

Requires the Administrator, every five years, to: (1) evaluate the effectiveness of the Program in, and identify best practices for, improving water quality, natural resources, and sustainable uses of estuaries covered by conferences; (2) assess the reasons why such practices resulted in the achievement of program goals; (3) identify and develop a plan for limiting redundant requirements for reporting by grant recipients; and (4) report on such evaluation to management conferences convened and the public.

Repeals provisions directing the Administrator to give priority to specified areas in the convening of conferences. 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.