6.400% SENIOR NOTES DUE 2018 SECOND SUPPLEMENTAL INDENTURE

Exhibit 4.2

Execution Version

MAGELLAN MIDSTREAM PARTNERS, L.P.

as Issuer

and

U.S. BANK NATIONAL ASSOCIATION

as Trustee

$250,000,000

6.400% SENIOR NOTES DUE 2018

SECOND SUPPLEMENTAL INDENTURE

Dated as of July 14, 2008

TABLE OF CONTENTS

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SECOND SUPPLEMENTAL INDENTURE dated as of July 14, 2008 (this “ Second Supplemental Indenture ”) between Magellan Midstream Partners, L.P., a Delaware limited partnership (the “ Partnership ” or the “ Issuer ”), and U.S. Bank National Association, a national banking association, as trustee (the “ Trustee ”).

W I T N E S S E T H:

WHEREAS, the Issuer has heretofore entered into an Indenture, dated as of April 19, 2007 (the “ Original Indenture ”), with U.S. Bank National Association, as trustee;

WHEREAS, the Original Indenture, as supplemented pursuant to this Second Supplemental Indenture, is herein called the “ Indenture ”;

WHEREAS, the Issuer proposes to create under the Indenture a new series of Debt Securities;

WHEREAS, the Issuer having heretofore entered into the First Supplemental Indenture dated as of April 19, 2007, in order to create an initial series of Debt Securities, the 6.400% Senior Notes due 2037;

WHEREAS, additional Debt Securities of other series hereafter established, except as may be limited in the Original Indenture as at the time supplemented and modified, may be issued from time to time pursuant to the Original Indenture as at the time supplemented and modified by a supplemental indenture; and

WHEREAS, all conditions necessary to authorize the execution and delivery of this Second Supplemental Indenture and to make it a valid and binding obligation of the Issuer have been done or performed;

NOW, THEREFORE, in consideration of the agreements and obligations set forth herein and for other good and valuable consideration, the sufficiency of which is hereby acknowledged, the parties hereto hereby agree as follows:

ARTICLE I

ESTABLISHMENT OF NEW SERIES

Section 1.01 Establishment of New Series . (a) There is hereby established a new series of Notes to be issued under the Indenture, to be designated as the Issuer’s 6.400% Senior Notes due 2018 (the “ Notes ”).

(b) There are to be authenticated and delivered $250,000,000 principal amount of Notes on the Issue Date, and from time to time thereafter there may be authenticated and delivered an unlimited principal amount of Additional Notes.

(c) The Notes shall be issued initially in the form of one or more Global Securities in substantially the form set out in Exhibit A hereto. The Depositary with respect to the Notes shall be The Depository Trust Company.

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(d) Initially, there shall be no Subsidiary Guarantors. Each Note shall be dated the date of authentication thereof and shall bear interest as provided in paragraph 1 of the form of Note in Exhibit A hereto.

(e) If and to the extent that the provisions of the Original Indenture are duplicative of, or in contradiction with, the provisions of this Second Supplemental Indenture, the provisions of this Second Supplemental Indenture shall govern.

ARTICLE II

DEFINITIONS AND INCORPORATION BY REFERENCE

Section 2.01 Definitions . All capitalized terms used herein and not otherwise defined below shall have the meanings ascribed thereto in the Original Indenture. The following are additional definitions used in this Second Supplemental Indenture:

“ Additional Notes ” has the meaning assigned to it in Section 3.02 hereof.

“ Consolidated Net Tangible Assets ” means, at any date of determination, the total amount of assets after deducting therefrom (1) all current liabilities (excluding (A) any current liabilities that by their terms are extendible or renewable at the option of the obligor thereon to a time more than 12 months after the time as of which the amount thereof is being computed, and (B) current maturities of long-term debt), and (2) the amount (net of any applicable reserves) of all goodwill, trade names, trademarks, patents and other like intangible assets, all as set forth on the consolidated balance sheet of the Partnership and its consolidated subsidiaries for the Partnership’s most recently completed fiscal quarter, prepared in accordance with GAAP.

“ Debt ” means any obligation created or assumed by any Person for the repayment of money borrowed, any purchase money obligation created or assumed by such Person and any guarantee of the foregoing.

“ Funded Debt ” means all Debt maturing one year or more from the date of the creation thereof, all Debt directly or indirectly renewable or extendible, at the option of the debtor, by its terms or by the terms of any instrument or agreement relating thereto, to a date one year or more from the date of the creation thereof, and all Debt under a revolving credit or similar agreement obligating the lender or lenders to extend credit over a period of one year or more.

“ Issue Date ” means the date on which the Notes are initially issued.

“ Lien ” means, as to any Person, any mortgage, lien, pledge, security interest or other encumbrance in or on, or adverse interest or title of any vendor, lessor, lender or other secured party to or of such Person under conditional sale or other title retention agreement or capital lease with respect to, any property or asset of such Person.

“ Notes ” has the meaning assigned to it in Section 1.01(a) hereof.

“ Permitted Liens ” means (1) Liens upon rights-of-way for pipeline purposes; (2) any statutory or governmental Lien, mechanics’, materialmen’s, carriers’ or similar Lien incurred in the ordinary course of business which is not yet due or which is being contested in good faith by

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appropriate proceedings and any undetermined Lien which is incidental to construction; (3) the right reserved to, or vested in, any municipality or public authority by the terms of any right, power, franchise, grant, license, permit or by any provision of law, to purchase or recapture or to designate a purchaser of, any property or assets; (4) Liens for taxes and assessments which are (A) for the then current year, (B) not at the time delinquent, or (C) delinquent but the validity of which is being contested at the time by the Partnership or any Restricted Subsidiary in good faith; (5) Liens arising under, or to secure performance of, leases, other than capital leases; (6) any Lien upon, or deposits of, any assets in favor of any surety company or clerk of court for the purpose of obtaining indemnity or stay of judicial proceedings; (7) any Lien upon property or assets acquired or sold by the Partnership or any Restricted Subsidiary resulting from the exercise of any rights arising out of defaults on receivables; (8) any Lien incurred in the ordinary course of business in connection with workmen’s compensation, unemployment insurance, temporary disability, social security, retiree health or similar laws or regulations or to secure obligations imposed by statute or governmental regulations; (9) any Lien in favor of the United States of America or any state thereof, or any other country, or any political subdivision of any of the foregoing, to secure partial, progress, advance or other payments pursuant to any contract or statute, or any Lien securing industrial development, pollution control or similar revenue bonds; or (10) any easements, exceptions or reservations in any property or assets of the Partnership or any Restricted Subsidiary granted or reserved for the purpose of pipelines, roads, the removal of oil, gas, coal or other minerals, and other like purposes, or for the joint or common use of real property, facilities and equipment, which are incidental to, and do not materially interfere with, the ordinary conduct of its business or the business of the Partnership and its Subsidiaries, taken as a whole.

“ Person ” means any individual, corporation, partnership, joint venture, limited liability company, association, joint-stock company, trust, other entity, unincorporated organization or government or other agency or political subdivision thereof.

“ Principal Property ” means any pipeline, terminal or terminal facility property or asset owned or leased by the Partnership or any Subsidiary, including any related property or asset employed in the transportation (including vehicles that generate transportation revenues), distribution, terminalling, gathering, treating, processing, marketing or storage of crude oil or refined petroleum products, natural gas, natural gas liquids, fuel additives, petrochemicals or ammonia, except, in the case of, (1) any property or asset consisting of inventories, furniture, office fixtures and equipment (including data processing equipment), vehicles and equipment used on, or useful with, vehicles (but excluding vehicles that generate transportation revenues as provided above), and (2) any such property or asset, plant or terminal which, in the opinion of the Board of Directors, is not material in relation to the activities of the Partnership and its Subsidiaries, taken as a whole.

“ Ratings Affirmation ” means, with respect to any particular action or proposed action, each of Standard & Poor’s Rating Services and Moody’s Investors Service, Inc. or, if either or both of such ratings agencies do not then rate the Notes, such other nationally recognized statistical rating organization (as defined in the rules and regulations of the SEC) then having issued long-term debt ratings for the Notes, affirms that such long-term debt ratings will not be lowered as a result of the taking of such action or proposed action.

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“ Restricted Subsidiary ” means any Subsidiary of the Partnership that owns or leases, directly or indirectly through ownership of or an ownership interest in another Subsidiary, any Principal Property.

“ Sale-Leaseback Transaction ” means the sale or transfer by the Partnership or any Restricted Subsidiary of any Principal Property to a Person (other than the Partnership or a Restricted Subsidiary) and the taking back by the Partnership or any Restricted Subsidiary, as the case may be, of a lease of such Principal Property.

“ Subsidiary ” means, with respect to any Person,

(1) any other Person of which more than 50% of the total voting power of capital interests (without regard to any contingency to vote in the election of directors, managers, trustees, or equivalent persons), at the time of such determination, is owned or controlled, directly or indirectly, by such Person or one or more of the Subsidiaries of such Person;

(2) in the case of a partnership, any Person of which more than 50% of the partners’ capital interests (considering all partners’ capital interests as a single class), at the time of such determination, is owned or controlled, directly or indirectly, by such Person or one or more of the Subsidiaries of such Person; or

(3) any other Person in which such Person or one or more of the Subsidiaries of such Person have the power to control, by contract or otherwise, the board of directors, managers, trustees or equivalent governing body of, or otherwise control, such other Person.

ARTICLE III

THE NOTES

Section 3.01 Form . The Notes shall be issued in the form of one or more Global Securities, and the Notes and Trustee’s certificate of authentication shall be substantially in the form of Exhibit A hereto, the terms of which are incorporated in and made a part of this Second Supplemental Indenture, and the Issuer and the Trustee, by their execution and delivery of this Second Supplemental Indenture, expressly agree to such terms and provisions and to be bound thereby.

Section 3.02 Issuance of Additional Notes . The Issuer may, from time to time, issue an unlimited amount of additional Notes (“ Additional Notes ”) under the Indenture, which shall be issued in the same form as the Notes issued on the Issue Date and which shall have identical terms as the Notes issued on the Issue Date other than with respect to the issue date, issue price and first payment of interest. The Notes issued on the Issue Date shall be limited in aggregate principal amount to $250,000,000. The Notes issued on the Issue Date and any Additional Notes subsequently issued shall be treated as a single series for purposes of giving of notices, consents, waivers, amendments and taking any other action permitted under the Indenture and for purposes of interest accrual and redemptions.

Section 3.03 Transfer of Notes . When Notes are presented to the Registrar with the request to register the transfer of such Notes or exchange such Notes for an equal principal amount of Notes of other authorized denominations, the Registrar shall register the transfer or make the exchange in accordance with Article II of the Original Indenture.

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Section 3.04 Restrictive Legend . Each security certificate evidencing the Global Securities shall bear a legend substantially in the form set forth in Section 2.15(a) of the Original Indenture.

ARTICLE IV

REDEMPTION

Section 4.01 Optional Redemption.

(a) At its option, the Issuer may choose to redeem all or any portion of the Notes, at once or from time to time.

(b) To redeem the Notes, the Issuer must pay a redemption price in an amount determined in accordance with the provisions of paragraph number 5 of the form of Note in Exhibit A hereto, plus accrued and unpaid interest, if any, to the Redemption Date (subject to the right of Holders on the relevant record date to receive interest due on the relevant interest payment date).

(c) Any redemption pursuant to this Section 4.01 shall be made pursuant to the provisions of Sections 3.01 through 3.03 of the Original Indenture. The actual redemption price, calculated as provided in paragraph number 5 of the form of Note in Exhibit A hereto, shall be certified in writing to the Issuer and the Trustee by the Independent Investment Banker (as defined in such paragraph 5) no later than two Business Days prior to each Redemption Date.

Section 4.02 Mandatory Redemption . The Issuer shall not be required to make mandatory redemption or sinking fund payments with respect to the Notes and shall have no obligation to repurchase any Notes at the option of the Holders.

ARTICLE V

COVENANT SUPPLEMENTS AND AMENDMENTS

Section 5.01 Covenants of the Partnership .

(a) Article IV of the Original Indenture is hereby supplemented, but only in relation to the Notes, by the addition of the following new Sections at the end of Article IV:

“Section 4.12. Subsidiary Guarantees . If any Subsidiary of the Partnership that is not then a Subsidiary Guarantor becomes a guarantor or co-obligor of any Funded Debt of the Partnership, in either case after the Issue Date, then the Partnership shall cause such Subsidiary to promptly execute and deliver a supplemental Indenture, substantially in the form of Exhibit B hereto, providing for the Guarantee of the payment of the Notes pursuant to Article XIV hereof.

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Section 4.13. Limitations on Liens . The Partnership will not, nor will it permit any Subsidiary to, create, assume, incur or suffer to exist any Lien upon any Principal Property or upon any capital stock of any Restricted Subsidiary, whether owned or leased on the date of this Indenture or thereafter acquired, to secure any Debt of the Partnership or any other Person (other than the Debt Securities issued hereunder), without in any such case making effective provision whereby all of the Debt Securities Outstanding hereunder shall be secured equally and ratably with, or prior to, such Debt so long as such Debt shall be so secured. This restriction shall not apply to or prevent the creation or existence of:

(a) any Lien on any property or assets of the Partnership or any Restricted Subsidiary in existence on the Issue Date or created pursuant to an “after-acquired property” clause or similar term in existence on the Issue Date in any mortgage, pledge agreement, security agreement or other similar instrument applicable to the Partnership or any Restricted Subsidiary and in existence on the Issue Date;

(b) any Lien on any property or assets created at the time of acquisition of such property or assets by the Partnership or any Restricted Subsidiary or within one year after such time to secure all or a portion of the purchase price for such property or assets or Debt incurred to finance such purchase price, whether such Debt was incurred prior to, at the time of or within one year of such acquisition;

(c) any Lien on any property or assets existing thereon at the time of the acquisition thereof by the Partnership or any Restricted Subsidiary (whether or not the obligations secured thereby are assumed by the Partnership or any Restricted Subsidiary), provided that such Lien only encumbers the property or assets so acquired;

(d) any Lien on any property or assets of a Person existing thereon at the time such Person becomes a Restricted Subsidiary by acquisition, merger or otherwise, provided that such Lien is not incurred in anticipation of such Person becoming a Restricted Subsidiary;

(e) any Lien on any property or assets to secure all or part of the cost of construction, development, repair or improvements thereon or to secure Debt incurred prior to, at the time of, or within one year after completion of such construction, development, repair or improvements or the commencement of full operations thereof (whichever is later), to provide funds for any such purpose;

(f) any Lien in favor of the Partnership or any Restricted Subsidiary;

(g) any Lien created or assumed by the Partnership or any Restricted Subsidiary in connection with the issuance of Debt the interest on which is excludable from gross income of the holder of such Debt pursuant to the Internal Revenue Code of 1986, as amended, or any successor statute, for the purpose of financing, in whole or in part, the acquisition or construction of property or assets to be used by the Partnership or any Subsidiary;

(h) Permitted Liens;

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(i) any Lien on any additions, improvements, replacements, repairs, fixtures, appurtenances or component parts thereof, attaching to or required to be attached to property or assets pursuant to the terms of any mortgage, pledge agreement, security agreement or other similar instrument, creating a Lien upon such property or assets permitted by Clauses (a) through (h), inclusive, of this Section; or

(j) any extension, renewal, refinancing, refunding or replacement (or successive extensions, renewals, refinancings, refundings or replacements) of any Lien, in whole or in part, that is referred to in Clauses (a) through (i), inclusive, of this Section, or of any Debt secured thereby; provided, however, that the principal amount of Debt secured thereby shall not exceed the greater of (1) the principal amount of Debt so secured at the time of such extension, renewal, refinancing, refunding or replacement (plus the aggregate amount of premiums, other payments, costs and expenses required to be paid or incurred in connection with such extension, renewal, refinancing, refunding or replacement) and (2) the maximum committed principal amount of Debt so secured at such time; provided further, however, that such extension, renewal, refinancing, refunding or replacement shall be limited to all or a part of the property or assets (including improvements, alterations and repairs on such property or assets) subject to the Lien so extended, renewed, refinanced, refunded or replaced (plus improvements, alterations and repairs on such property or assets).

Notwithstanding the foregoing provisions of this Section, the Partnership may, and may permit any Subsidiary to, create, assume, incur or suffer to exist any Lien upon any Principal Property or capital stock of a Restricted Subsidiary to secure Debt of the Partnership or any other Person (other than the Debt Securities) that is not excepted by Clauses (a) through (j), inclusive, of this Section without securing the Debt Securities issued hereunder, provided that the aggregate principal amount of all Debt then outstanding secured by such Lien and all other Liens not excepted by Clauses (a) through (j), inclusive, of this Section, together with all net sale proceeds from Sale-Leaseback Transactions (excluding Sale-Leaseback Transactions permitted by Clauses (a) through (d), inclusive, of Section 4.14), does not exceed at any one time 15% of Consolidated Net Tangible Assets.

Section 4.14. Restriction of Sale-Leaseback Transaction . The Partnership will not, nor will it permit any Restricted Subsidiary to, engage in a Sale-Leaseback Transaction, unless:

(a) the Sale-Leaseback Transaction occurs within one year from the date of acquisition of the Principal Property subject thereto or the date of the completion of construction or commencement of full operations on such Principal Property, whichever is later;

(b) the Sale-Leaseback Transaction involves a lease for a period, including renewals, of not more than three years;

(c) the Partnership or such Restricted Subsidiary would be entitled under Section 4.13 to i