<PAGE>
                                                               EXECUTION VERSION

                                                                   Exhibit 10.16

                 SECOND AMENDMENT AND WAIVER TO CREDIT AGREEMENT

            SECOND AMENDMENT AND WAIVER, dated as of December 28, 2004 (this
"Second Amendment"), to the Credit Agreement, dated as of May 28, 2004 (as
amended by the First Amendment, dated as of August 6, 2004, and as otherwise
amended, supplemented or modified from time to time, the "Credit Agreement"),
among ANR HOLDINGS, LLC, a Delaware limited liability company ("Holdings"),
ALPHA NATURAL RESOURCES, LLC, a Delaware limited liability company (the
"Borrower"), the LENDERS from time to time party thereto, CITICORP NORTH
AMERICA, INC., as administrative agent (in such capacity, the "Administrative
Agent") and as collateral agent (in such capacity, the "Collateral Agent"),
CREDIT SUISSE FIRST BOSTON, acting through its Cayman Islands Branch, as
syndication agent (in such capacity, the "Syndication Agent"), UBS SECURITIES
LLC, as documentation agent (in such capacity, the "Documentation Agent"),
CREDIT SUISSE FIRST BOSTON, acting through its Cayman Islands Branch, UBS
SECURITIES LLC and CITIGROUP GLOBAL MARKETS INC., as joint lead arrangers (in
such capacities, collectively, the "Arrangers"), and CREDIT SUISSE FIRST BOSTON,
acting through its Cayman Islands Branch, and UBS SECURITIES LLC, as joint
bookrunners (in such capacities, collectively, the "Bookrunners").

                              W I T N E S S E T H:

            WHEREAS, Holdings, the Borrower and the Administrative Agent, among
others, are parties to the Credit Agreement;

            WHEREAS, Holdings and the Borrower have requested that the Lenders
agree to amend certain provisions of the Credit Agreement and to waive certain
Defaults as set forth in this Second Amendment; and

            WHEREAS, the Lenders whose signatures appear below, constituting at
least the Required Lenders, are willing to amend the Credit Agreement and to
waive certain Defaults thereunder on the terms and subject to the conditions set
forth herein;

            NOW, THEREFORE, for good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, and in consideration of the
premises contained herein, the parties hereto agree as follows:

            1.    Defined Terms. Capitalized terms used herein and not otherwise
defined herein shall have the meanings ascribed to such terms in the Credit
Agreement.

            2.    Amendment to Section 1.01 (Defined Terms). Section 1.01 of the
Credit Agreement is hereby amended by adding the following words to the
definition of "Net Cash Proceeds" immediately prior to the proviso in clause
(iii) thereof:

            "or which is secured by the proceeds of such Recovery Event as
permitted by Section 6.02(p) and which is required to be repaid with such
proceeds;"
<PAGE>

            3.    Amendment to Section 6.01 (Indebtedness). Section 6.01 of the
Credit Agreement is hereby amended by adding the following clause (m) at the end
of such Section:

            "and (m) Indebtedness relating to the financing of insurance policy
premiums; provided that (i) such insurance is for the benefit of the
Loan Parties and (ii) the aggregate principal amount of Indebtedness permitted
by this Section 6.01(m) shall not exceed $25,000,000 at any time outstanding."

            4.    Amendment to Section 6.02 (Liens). Section 6.02 of the Credit
Agreement is hereby amended by adding the following clause (p) at the end of
such Section:

            "and (p) Liens on insurance policy proceeds; provided that such
Liens secure Indebtedness permitted by Section 6.01(m)."

            5.    Waiver. The Required Lenders hereby waive for all periods from
the Closing Date through the Second Amendment Effective Date (as defined below)
(i) the provisions of Section 6.02 of the Credit Agreement to the extent such
provisions prohibit Liens securing the note payable to Cananwill Finance for the
financing of certain insurance premiums as set forth on Schedule 6.01 and (ii)
any Default or Event of Default that may have arisen by reason of the existence
of such Liens.

            The waivers set forth in this Section 5 shall be effective only as
to the matters set forth specifically herein and shall not entitle the Borrower
to any other waiver or agreement with respect to any other matter.

            6.    Representations and Warranties. In order to induce the other
parties hereto to enter into this Second Amendment, Holdings and the Borrower
represent and warrant to each other party hereto that, after giving effect to
this Second Amendment (a) the representations and warranties set forth in each
of the Loan Documents shall be true and correct in all material respects on and
as of the date hereof with the same effect as though made on and as of such
date, except to the extent such representations and warranties relate to an
earlier date, in which case such representations and warranties shall be true
and correct in all material respects on and as of such earlier date; provided
that the references to the Credit Agreement in such representations and
warranties shall be deemed to refer to the Credit Agreement as amended pursuant
to this Second Amendment; and (b) no Event of Default or Default shall have
occurred and be continuing.

            7.    Conditions to Effectiveness of this Second Amendment. This
Second Amendment shall become effective on the date (the "Second Amendment
Effective Date") on which:

            (a)   The Administrative Agent shall have received duly executed and
delivered counterparts of this Second Amendment that, when taken together, bear
the signatures of Holdings, the Borrower and the Required Lenders;

            (b)   The Borrower shall have paid to the Administrative Agent all
outstanding fees, costs and expenses owing to the Administrative Agent as of
such date; and

                                       2

<PAGE>

            (c)   The Administrative Agent shall have received such additional
documentation as the Administrative Agent may reasonably require.

            8.    Continuing Effect; No Other Amendments. Except as expressly
set forth in this Second Amendment, all of the terms and provisions of the
Credit Agreement are and shall remain in full force and effect and each of
Holdings and the Borrower shall continue to be bound by all of such terms and
provisions. The amendments provided for herein are limited to the specific
subsections of the Credit Agreement specified herein and shall not constitute an
amendment of, or an indication of the Administrative Agent's or the Lenders'
willingness to amend or waive, any other provisions of the Credit Agreement or
the same subsections for any other date or purpose. This Second Amendment shall
constitute a Loan Document.

            9.    Expenses. The Borrower agrees to pay and reimburse the
Administrative Agent for all its reasonable out-of-pocket costs and expenses
incurred in connection with the development, preparation and execution and
delivery of this Second Amendment, and any other documents prepared in
connection herewith, and the transactions contemplated hereby, including,
without limitation, reasonable fees and disbursements and other charges of
counsel to the Administrative Agent and the charges of IntraLinks.

            10.   Counterparts. This Second Amendment may be executed by one or
more of the parties to this Second Amendment on any number of separate
counterparts and all of said counterparts taken together shall be deemed to
constitute one and the same instrument. Delivery of an executed signature page
of this Second Amendment by facsimile transmission shall be effective as
delivery of a manually executed counterpart hereof. A set of the copies of this
Second Amendment signed by all the parties shall be lodged with the Borrower and
the Administrative Agent. The execution and delivery of this Second Amendment by
the Borrower, the Lenders party hereto and the Administrative Agent shall be
binding upon the Loan Parties, the Lenders, the Agents and all future holders of
the Loans.

            11.   Effect of Amendment. On the Second Amendment Effective Date,
the Credit Agreement shall be amended as provided herein. The parties hereto
acknowledge and agree that (a) this Second Amendment and any other Loan
Documents executed and delivered in connection herewith do not constitute a
novation, or termination of the "Obligations" (as defined in the Credit
Agreement) under the Credit Agreement as in effect prior to the Second Amendment
Effective Date; (b) such "Obligations" are in all respects continuing (as
amended hereby) with only the terms thereof being modified to the extent
provided in this Second Amendment; and (c) the Liens and security interests as
granted under the Security Documents securing payment of such "Obligations" are
in all respects continuing and in full force and effect and secure the payment
of the "Obligations".

            12.   GOVERNING LAW. THIS SECOND AMENDMENT AND THE RIGHTS AND
OBLIGATIONS OF THE PARTIES UNDER THIS SECOND AMENDMENT SHALL BE GOVERNED BY, AND
CONSTRUED AND INTERPRETED IN ACCORDANCE WITH, THE LAW OF THE STATE OF NEW YORK.

                            [Signature Pages Follow]

                                       3

<PAGE>

            IN WITNESS WHEREOF, the parties hereto have caused this Second
Amendment to be executed and delivered by their respective duly authorized
officers as of the date first above written.

                                                 ANR HOLDINGS, LLC

                                                 By:    /s/ Michael J. Quillen
                                                     ---------------------------
                                                        Name: Michael J. Quillen
                                                        Title: President

                                                 ALPHA NATURAL RESOURCES, LLC

                                                 By: /s/ Michael J. Quillen
                                                     ---------------------------
                                                        Name: Michael J. Quillen
                                                        Title: President

                                                 CITICORP NORTH AMERICA, INC.,

                                                 as Administrative Agent

                                                 By:    /s/ Daniel J. Miller
                                                     ---------------------------
                                                        Name: Daniel J. Miller
                                                        Title: Vice President

<PAGE>

SIGNATURE PAGE TO SECOND AMENDMENT DATED AS OF DECEMBER 27, 2004, TO THE ALPHA
NATURAL RESOURCES, LLC CREDIT AGREEMENT DATED AS OF MAY 28, 2004, AS AMENDED

To Approve the Second Amendment:

Name of Institution: Branch Banking and Trust Company

By: /s/ Hugh Ferguson
   ---------------------
Name: Hugh Ferguson
Title: Vice President

<PAGE>

SIGNATURE PAGE TO SECOND AMENDMENT DATED AS OF DECEMBER 28, 2004, TO THE ALPHA
NATURAL RESOURCES, LLC CREDIT AGREEMENT DATED AS OF MAY 28, 2004, AS AMENDED

To Approve the Second Amendment:

Name of Institution:

CITICORP NORTH AMERICA, INC.

By: /s/ Daniel J. Miller
    ---------------------
Name: Daniel J. Miller
Title: Vice President

<PAGE>

SIGNATURE PAGE TO SECOND AMENDMENT DATED AS OF DECEMBER 28, 2004, TO THE ALPHA
NATURAL RESOURCES, LLC CREDIT AGREEMENT DATED AS OF MAY 28, 2004, AS AMENDED

To Approve the Second Amendment:

Name of Institution:
Credit Suisse First Boston,
acting through it Cayman Islands Branch

By: /s/ Vanessa Gomez
    --------------------
Name: Vanessa Gomez
Title:  Associate

By: /s/ Thomas S. Hall
    --------------------
Name: Thomas S. Hall
Title: Vice President

<PAGE>

SIGNATURE PAGE TO SECOND AMENDMENT DATED AS OF DECEMBER 28, 2004, TO THE ALPHA
NATURAL RESOURCES, LLC CREDIT AGREEMENT DATED AS OF MAY 28, 2004, AS AMENDED

To Approve the Second Amendment:

Name of Institution: Madison Capital Funding, LLC

By: /s/ Craig Lacy
   ----------------------
Name: Craig Lacy
Title: Managing Director

<PAGE>

SIGNATURE PAGE TO SECOND AMENDMENT DATED AS OF DECEMBER 28, 2004, TO THE ALPHA
NATURAL RESOURCES, LLC CREDIT AGREEMENT DATED AS OF MAY 28, 2004, AS AMENDED

To Approve the Second Amendment:

PNC Bank, National Association

By: /s/ Dale A. Stein
   ------------------
Name: Dale A. Stein
Title: Senior Vice President

<PAGE>

SIGNATURE PAGE TO SECOND AMENDMENT DATED AS OF DECEMBER 28, 2004, TO THE ALPHA
NATURAL RESOURCES, LLC CREDIT AGREEMENT DATED AS OF MAY 28, 2004, AS AMENDED

To Approve the Second Amendment:

Name of Institution: UBS Loan Finance LLC

By: /s/ Barbara Ezell-McMichael
    -----------------------------------
Name: Barbara Ezell-McMichael
Title: Associate Director
       Banking Products Services US

By: /s/ Winslowe Ogbourne
    -----------------------------------
Name: Barbara Ezell-McMichael
Title: Associate Director
       Banking Products Services US