Clean Estuaries Act of 2014

Clean Estuaries Act of 2014 - (Sec. 2) Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to revise, and reauthorize through FY2019, the National Estuary Program.

Expands the purposes of management conferences for estuary programs, including by adding components that must be included in a Comprehensive Conservation and Management Plan (Plan).

Requires management conferences to make use of collaborative processes in updating or developing a Plan.

Establishes a process by which a state may resubmit a Plan that the Environmental Protection Agency (EPA) has determined is incomplete.

Considers a submission or resubmission of a Plan to be approved if the EPA fails to respond within 120 days of receiving it. Requires the EPA to terminate a management conference if the conference fails to submit a Plan within three years of being convened.

Requires the EPA to: (1) evaluate, every five years, the implementation of each Plan developed 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 the report publicly available. Requires management conferences to update plans within 18 months after they are evaluated.

Authorizes the EPA 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 EPA 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 appropriate federal agencies, after the EPA's approval of a Plan, to cooperate and to coordinate activities related to implementation. Makes the 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.

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

Requires the EPA to evaluate and report to the public on the National Estuary Program every five years.