Water Pollution Control and Estuary Restoration Financing Act

Water Pollution Control and Estuary Restoration Financing Act - Amends the Federal Water Pollution Control Act to extend the authorization of appropriations for the State water pollution control revolving fund program through FY 2000.

Requires a specified percentage (increasing with each succeeding fiscal year) of such appropriations to be used for capitalization grants for estuary plans to qualified States. Makes States that fail to submit approved need estimates ineligible for assistance.

Directs States to establish separate Estuary Accounts in their water pollution control revolving funds, to be used for implementing approved estuary plans. Permits loans made with Account funds to be for terms of up to 40 years or for the useful life of a facility constructed with the loan, whichever is less, if the borrower demonstrates financial hardship. Establishes a State matching requirement for deposits into Accounts.

Authorizes the Administrator of the Environmental Protection Agency to make grants for the implementation of estuary conservation and management plans. Authorizes appropriations.

Permits certain grants under the National Estuary Program to be used for interim actions adopted by management conferences to protect the water and sediment quality of estuaries.

Extends the authorization of appropriations for management conferences, grants, conservation and management plans, and research under the National Estuary Program through FY 2000.

Directs the Administrator to issue a guidance document establishing requirements for: (1) management conferences to follow in developing, implementing, and monitoring conservation and management plans; and (2) approving and implementing interim actions to protect water quality of estuaries for which plans are developed.

Requires management conferences to be convened for periods of at least five years (currently, up to five years). Permits extensions for an additional five years if the affected Governors concur and the extension is necessary to meet requirements. Revises approval and implementation procedures for estuary conservation and management plans and establishes procedures for interim actions.