<PAGE>

                                                                     EXHIBIT 3.1

                                                                  EXECUTION COPY

                                    AMENDMENT
                                       TO
            AMENDED AND RESTATED LIMITED LIABILITY COMPANY AGREEMENT
                    OF AMERICAN COMMERCIAL LINES HOLDINGS LLC

            This AMENDMENT, dated as of May 29, 2002, is to the AMENDED AND
RESTATED LIMITED LIABILITY COMPANY AGREEMENT of American Commercial Lines
Holdings LLC, a Delaware limited liability company (the "Company"), by and among
those parties signatory hereto, such parties being members of the Company
(collectively referred to as the "Members" or individually as a "Member").
Capitalized terms used but not otherwise defined herein shall have the meanings
assigned to such terms in the Prior Agreement (as defined below).

            WHEREAS, the Company (of which CSX was the initial member) was
formed on February 3, 1998 pursuant to and in accordance with the Act; and

            WHEREAS, in accordance with the Act and the Limited Liability
Company Agreement of the Company, dated as of February 3, 1998, as amended and
restated as of March 30, 1998, as further amended and restated as of June 30,
1998 and April 27, 1999, and as amended as of September 8, 2001 (the "Prior
Agreement"), the Members desire to, and hereby, clarify and, to the extent
necessary, amend the Prior Agreement as set forth herein; and

            WHEREAS, this Amendment is made pursuant to Section 12.6 of the
Prior Agreement and has been approved by the Board and is executed by a majority
of the holders of each class of Units, including all CSX Members and all Vectura
Parties and their Permitted Transferees.

            NOW, THEREFORE, the parties hereto, intending to be legally bound,
hereby agree as follow:

                                   ARTICLE I
                          AMENDMENTS TO PRIOR AGREEMENT

            Section 1.1 Definitions. Section 1.1 of the Prior Agreement is
hereby amended to add the following defined term thereto in the appropriate
alphabetical order:

            "2002 Recapitalization Agreement" means the Recapitalization
            Agreement, dated as of March 15, 2002, by and among the Company,
            ACL, all of the Members holding Preferred Units and Common Units
            listed on the signature pages thereto, certain of the Members
            holding only Common Units, and Danielson Holding Corporation, as
            amended by the First Amendment to Recapitalization Agreement, dated
            as of May 29, 2002 (as further amended, restated or modified from
            time to time)."
<PAGE>
            Section 1.2 Transfers of Units.

                  (a) The first sentence of Section 8.1(a) of the Prior
Agreement is hereby amended and restated as follows:

                  "No Unitholder shall Transfer any Units other than in
            accordance with the terms and conditions of this Article VIII and
            the other provisions of this Agreement; provided, that,
            notwithstanding any other provision of this Agreement and without
            the consent of any other Person, any Unitholder may abandon any or
            all of its Units to the Company in exchange for no consideration."

                  (b) Article VIII of the Prior Agreement is hereby amended to
add the following new Section 8.9 thereto:

                  "8.9 2002 Recapitalization Transactions. Notwithstanding any
            other provision of this Agreement, including without limitation
            Article VIII hereof, (a) the Company is hereby authorized to
            execute, deliver and perform that certain 2002 Recapitalization
            Agreement, and all documents, instruments, certificates and other
            agreements contemplated thereby or related thereto, and (b) the
            Company is hereby authorized to consummate all transactions
            contemplated by or related to the Recapitalization Agreement,
            including, without limitation, the Common Unit Surrender (as defined
            in the 2002 Recapitalization Agreement), the Management Unitholder
            Abandonment (as defined in the 2002 Recapitalization Agreement), the
            Merger (as defined in the 2002 Recapitalization Agreement), and the
            DHC Preferred Exchange (as defined in the 2002 Recapitalization
            Agreement), all without any further vote, approval or action of any
            Member or other Person being required. In connection with the
            foregoing, and without limiting the foregoing authorization, and
            notwithstanding any other provision of this Agreement, (i) any
            Officer is hereby authorized, on behalf of the Company, to execute
            and deliver the 2002 Recapitalization Agreement and all documents,
            instruments, certificates and other agreements contemplated thereby
            or related thereto, (ii) the Company's chief executive officer is
            hereby designated an authorized person within the meaning of the Act
            to execute and file a certificate of merger with the Delaware
            Secretary of State, and (iii) the Company may issue limited
            liability company interests in the Company to any other Person and
            such Person may be admitted to the Company as a Member of the
            Company and may continue the Company without dissolution, all
            without any further vote, approval or action of any Member or other
            Person being required."


                                       2
<PAGE>
            Section 1.3 Prior Agreement. Except as expressly amended hereby, the
terms of the Prior Agreement are reaffirmed and unchanged.

                                   ARTICLE II
                                  MISCELLANEOUS

            SECTION 2.1 WAIVER OF JURY TRIAL. EACH OF THE PARTIES HERETO WAIVES
TO THE FULLEST EXTENT PERMITTED BY LAW ANY RIGHT IT MAY HAVE TO TRIAL BY JURY IN
RESPECT OF ANY CLAIM, DEMAND, ACTION OR CAUSE OF ACTION BASED ON, OR ARISING OUT
OF, UNDER OR IN CONNECTION WITH THIS AMENDMENT, OR ANY COURSE OF CONDUCT, COURSE
OF DEALING, VERBAL OR WRITTEN STATEMENT OR ACTION OF ANY PARTY HERETO, IN EACH
CASE WHETHER NOW EXISTING OR HEREAFTER ARISING, AND WHETHER IN CONTRACT, TORT,
EQUITY OR OTHERWISE. THE PARTIES TO THIS AMENDMENT EACH HEREBY AGREES THAT ANY
SUCH CLAIM, DEMAND, ACTION OR CAUSE OF ACTION SHALL BE DECIDED BY COURT TRIAL
WITHOUT A JURY AND THAT THE PARTIES TO THIS AMENDMENT MAY FILE AN ORIGINAL
COUNTERPART OR A COPY OF THIS AMENDMENT WITH ANY COURT AS EVIDENCE OF THE
CONSENT OF THE PARTIES HERETO TO THE WAIVER OF THEIR RIGHT TO TRIAL BY JURY.

            SECTION 2.2 GOVERNING LAW. ALL ISSUES AND QUESTIONS CONCERNING THE
APPLICATION, CONSTRUCTION, VALIDITY, INTERPRETATION AND ENFORCEMENT OF THIS
AMENDMENT SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE
STATE OF DELAWARE AND THE DELAWARE LIMITED LIABILITY COMPANY ACT, DELAWARE CODE,
TITLE 6, SECTIONS 18-101, ET SEQ., AS IN EFFECT FROM TIME TO TIME, WITHOUT
GIVING EFFECT TO ANY CHOICE OF LAW OR CONFLICT OF LAW PROVISION OR RULE (WHETHER
OF THE STATE OF DELAWARE OR ANY OTHER JURISDICTION) THAT WOULD CAUSE THE
APPLICATION OF THE LAWS OF ANY JURISDICTION OTHER THAN THE STATE OF DELAWARE.

            Section 2.3 Descriptive Headings. The descriptive headings of this
Amendment are inserted for convenience only and do not constitute a part of this
Amendment.

            Section 2.4 Severability. Whenever possible, each provision of this
Amendment shall be interpreted in such manner as to be effective and valid under
applicable law, but if any provision of this Amendment is held to be invalid,
illegal or unenforceable in any respect under any applicable law or rule in any
jurisdiction, such invalidity, illegality or unenforceability shall not affect
any other provision or any other jurisdiction, but this Amendment shall be
reformed, construed and enforced in such jurisdiction as if such invalid,
illegal or unenforceable provision had never been contained herein. The Members
shall negotiate in good faith to replace any provision so held to be invalid or
unenforceable so as to implement most effectively the transactions contemplated
by such provision in accordance with the original intent of the Members
signatory hereto.


                                       3
<PAGE>
            Section 2.5 Gender and Number. Whenever required by the context, the
singular number shall include the plural number, the plural number shall include
the singular number, the masculine gender shall include the neuter and feminine
genders and vice versa.

            Section 2.6 Counterparts. This Amendment may be executed in one or
more counterparts, each of which when executed and delivered shall be an
original, and all of which when executed shall constitute one and the same
instrument.

            Section 2.7 Entire Agreement. This Amendment, the Prior Agreement
and the other Transaction Documents embody the complete agreement and
understanding among the parties hereto with respect to the subject matter hereof
and supersede and preempt any prior understandings, agreements or
representations by or among the parties, written or oral, which may have related
to the subject matter hereof in any way.

            Section 2.8 No Waiver of Remedies. The failure of a Member to insist
on the strict performance of any covenant or duty required by this Amendment, or
to pursue any remedy under this Amendment, shall not constitute a waiver of the
breach or the remedy.

            Section 2.9 Remedies Cumulative. The remedies of the Members under
this Amendment are cumulative and shall not exclude any other remedies to which
the Member may be lawfully entitled. Each of the parties confirms that damages
at law may be an inadequate remedy for a breach or threatened breach of any
provision hereof. The respective rights and obligations hereunder shall be
enforceable by specific performance, injunction or other suitable remedy, but
nothing herein contained is intended to or shall limit or affect any rights at
law or by statute or otherwise of any party aggrieved as against the other
parties for a breach or threatened breach of any provision hereof, it being the
intention by this Section to make clear the agreement of the parties that the
respective rights and obligations of the parties hereunder shall be enforceable
in equity as well as at law or otherwise.

            Section 2.10 Binding Effect. This Amendment shall be binding upon
and inure to the benefit of all of the Members and their permitted successors,
legal representatives, and assigns.

                                      * * *


                                       4
<PAGE>
            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:

                                        By: /s/ David H. Baggs
                                            ------------------------------------
                                            Name: David H. Baggs
                                            Title: Vice President
                                            Brown Water Transportation Corp.


                                        AMERICAN COMMERCIAL LINES HOLDINGS LLC


                                        /s/ Michael C. Hagan
                                        ----------------------------------------
                                        Michael C. Hagan
                                        President

                                        399 VENTURE PARTNERS, INC.

                                        By:  /s/ David F. Thomas
                                             -----------------------------------
                                             Name: David F. Thomas
                                             Title:


                                        NATIONAL MARINE, LLC

                                        By:
                                             -----------------------------------
                                             Name:
                                             Title:


                                        CCT PARTNERS III, L.P.

                                        By:  CCT I Corporation
                                        Its: General Partner

                                        By:  /s/ William T. Comfort
                                             -----------------------------------
                                             Name: William T. Comfort
                                             Title:


                                        CCT PARTNERS V, L.P.

                                        By:  CCT 1998 Corporation
                                        Its: General Partner

                                        By:  /s/ William T. Comfort
                                             -----------------------------------
                                             Name: William T. Comfort
                                             Title:


                                        63 BR PARTNERSHIP

                                        By:  /s/ James A. Urry
                                             -----------------------------------
                                             Name:
                                             Title: Atty-in-fact

                                        NATIONAL MARINE, LLC


                                        By:  /s/ David Wagstaff III
                                             -----------------------------------
                                             Name: David Wagstaff III
                                             Title: President

                                        /s/ Steven A. Anderson
                                        ----------------------------------------
                                        Steven A. Anderson

                                        /s/ Stuart Agranoff
                                        ----------------------------------------
                                        Stuart Agranoff
<PAGE>
                                        MEMBER SIGNATURE PAGE


                                        /s/ Richard L. Huber
                                        ----------------------------------------
                                        Richard L. Huber

                                        /s/ David Wagstaff III
                                        ----------------------------------------
                                        David Wagstaff III

                                        /s/ Richard E. Mayberry, Jr.
                                        ----------------------------------------
                                        Richard E. Mayberry, Jr.


                                        /s/ David F. Thomas
                                        ----------------------------------------
                                        David F. Thomas


                                        Thomas F. McWilliams
                                        Flint Trust, dated 1 /27/98


                                        By:
                                             -----------------------------------
                                             Name: Jeanne Blasberg
                                             Title: Trustee


                                        ALCHEMY L.P.


                                        By:  /s/ Thomas F. McWilliams
                                             -----------------------------------
                                             Name:
                                             Title: G. P.


                                        /s/ John D. Weber
                                        ----------------------------------------
                                        John D. Weber


                                        /s/ Byron L. Knief
                                        ----------------------------------------
                                        Byron L. Knief


                                        /s/ James A. Urry
                                        ----------------------------------------
                                        James A. Urry

                                        THOMAS F. McWILLIAMS FLINT TRUST


                                        By: /s/ Jeanne Blasberg, Trustee
                                            ----------------------------
                                                Jeanne Blasberg, Trustee
<PAGE>
                                        /s/ Richard Cashin
                                        ----------------------------------------
                                        Richard Cashin

                                        /s/ Michael A. Delaney
                                        ----------------------------------------
                                        Michael A. Delaney


                                        /s/ Joseph M. Silvestri
                                        ----------------------------------------
                                        Joseph M. Silvestri


                                        /s/ David Y. Howe
                                        ----------------------------------------
                                        David Y. Howe


                                        /s/ M. Saleem Muqaddam
                                        ----------------------------------------
                                        M. Saleem Muqaddam


                                        /s/ Michael T. Bradley
                                        ----------------------------------------
                                        Michael T. Bradley


                                        /s/ Ian D. Highet
                                        ----------------------------------------
                                        Ian D. Highet
<PAGE>
            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Michael C. Hagan
                                             -----------------------------------
                                             Name: Michael C. Hagan

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ W. Norb Whitlock
                                             -----------------------------------
                                             Name: W. Norb Whitlock

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ James J. Wolff
                                             -----------------------------------
                                             Name: James J. Wolff

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Michael A. Khouri
                                             -----------------------------------
                                             Name: Michael A. Khouri
<PAGE>
            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Martin K. Pepper
                                             -----------------------------------
                                             Name: Martin K. Pepper

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Paul S. Besson
                                             -----------------------------------
                                             Name: Paul S. Besson

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ James F. Farley
                                             -----------------------------------
                                             Name: James F. Farley

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Christian Brinkop
                                             -----------------------------------
                                             Name: Christian Brinkop
<PAGE>
            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ C. William Kinzeler
                                             -----------------------------------
                                             Name: C. William Kinzeler

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Stephen J. Brooks
                                             -----------------------------------
                                             Name: Stephen J. Brooks

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Robert G. Burns
                                             -----------------------------------
                                             Name: Robert G. Burns

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Robert P. Herre
                                             -----------------------------------
                                             Name: Robert P. Herre
<PAGE>
            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Danny Irby
                                             -----------------------------------
                                             Name: Danny Irby

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ David D. Jahnke
                                             -----------------------------------
                                             Name: David D. Jahnke

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Daniel Jaworski
                                             -----------------------------------
                                             Name: Daniel Jaworski

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment. effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Peter L. Kazunas
                                             -----------------------------------
                                             Name: Peter L. Kazunas

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ R. Barker Price
                                             -----------------------------------
                                             Name: R. Barker Price
<PAGE>
            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ Paul F. Brotzge
                                             -----------------------------------
                                             Name: Paul F. Brotzge

            IN WITNESS WHEREOF, the Members of American Commercial Lines
Holdings LLC, a Delaware limited liability company, have executed this
Amendment, effective as of the date first written above.

                                        MEMBER:


                                        By:  /s/ James M. Fox
                                             -----------------------------------
                                             Name: James M. Fox

                                        MEMBER SIGNATURE PAGE

                                        TREETOPS LLC


                                        By:  /s/ David Wagstaff III
                                             -----------------------------------
                                             Name: David Wagstaff III
                                             Title: Manager

                                        MEMBER SIGNATURE PAGE

                                        CCT PARTNERS III, L.P.

                                        By:  CCT I Corporation
                                        Its: General Partner


                                        By:  /s/ William T. Comfort
                                             -----------------------------------
                                             Name: William T. Comfort
                                             Title:

                                        AMERICAN COMMERCIAL LINES LLC


                                        /s/ Michael C. Hagan
                                        ----------------------------------------
                                        Michael C. Hagan