Clean Water Trust Act of 2005

Clean Water Trust Act of 2005 - Amends the Federal Water Pollution Control Act (FWPCA) to establish in the Treasury the Clean Water Trust Fund, to be funded by user fees, to finance certain FWPCA programs and activities, including: (1) water pollution reduction and control; (2) technical assistance for small rural communities; (3) the National Center for Utility Management; (4) grants to states and interstate agencies to assist in the management of pollution control programs; (5) watershed pilot projects; (6) regional water pollution control; (7) alternative water source projects; (8) sewer overflow control; (9) fisheries habitat protection, restoration, and enhancement; and (10) wetlands restoration.

Authorizes the Administrator of the Environmental Protection Agency (EPA) to make grants to nonprofit organizations to: (1) provide technical assistance to rural and small municipalities for wastewater infrastructure financing; and (2) establish a National Center for Utility Management to promote improved management of public wastewater utilities.

Revises: (1) eligibility requirements for grants for sewage collection systems; and (2) state water pollution revolving fund provisions. Establishes a grant program under FWPCA to address the most serious water pollution problems.

Authorizes the Administrator to: (1) make grants to states, nonprofit organizations, and other entities for fresh water, estuarine, and marine fisheries habitat protection, preservation, and restoration; and (2) make grants to states for wetlands restoration.

Revises funding allocations for state water pollution control projects and activities serving Indian tribes and reservations.