Exhibit 4.1

FIRST SUPPLEMENTAL INDENTURE (this “ First Supplemental Indenture ”), dated as of January 8, 2014, among Navios Maritime Acquisition Corporation, a Marshall Islands corporation, (the “ Company ”), Navios Acquisition Finance (US) Inc., a Delaware corporation (together with the Company, the “ Co-Issuers ”), and Lefkada Shipping Corporation, Kerkyra Shipping Corporation, and Zakynthos Shipping Corporation, (each a “ Guaranteeing Subsidiary ”), each a Marshall Islands corporation and an indirect subsidiary of the Company, the other Guarantors (as defined in the Indenture referred to herein) and Wells Fargo Bank, National Association, as trustee (or its permitted successor) under the Indenture referred to below (the “ Trustee ”) and as collateral trustee (or its permitted successor) under the Indenture referred to below (the “ Collateral Trustee ”).

WITNESSETH

WHEREAS, the Co-Issuers and the Guarantors have heretofore executed and delivered to the Trustee an indenture (the “ Indenture ”), dated as of November 13, 2013 providing for the issuance of 8.125% First Priority Ship Mortgage Notes due 2021 (the “ Notes ”);

WHEREAS, the Indenture provides that under certain circumstances each Guaranteeing Subsidiary shall execute and deliver to the Trustee a supplemental indenture pursuant to which each Guaranteeing Subsidiary shall unconditionally guarantee all of the Co-Issuers’ obligations under the Notes and the Indenture on the terms and conditions set forth herein (the “ Note Guarantee ”); and

WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and deliver this First Supplemental Indenture.

NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the receipt of which is hereby acknowledged, each Guaranteeing Subsidiary and the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows:

1. CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the meanings assigned to them in the Indenture.

2. AGREEMENT TO GUARANTEE. Each Guaranteeing Subsidiary hereby agrees to provide an unconditional Guarantee, on and subject to the terms, conditions and limitations set forth in the Notation of Guarantee and in the Indenture, including, but not limited, to Article Ten thereof.

4. NEW YORK LAW TO GOVERN. THIS FIRST SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK, WITHOUT GIVING EFFECT TO CONFLICTS OF LAW PRINCIPLES TO THE EXTENT THAT THE APPLICATION OF THE LAWS OF ANOTHER JURISDICTION WOULD BE REQUIRED THEREBY.

5. COUNTERPARTS. The parties may sign any number of copies of this First Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement.

6. EFFECT OF HEADINGS. The Section headings herein are for convenience only and shall not affect the construction hereof.

7. THE TRUSTEE. The Trustee shall not be responsible in any manner whatsoever for or in respect of the validity or sufficiency of this First Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by each Guaranteeing Subsidiary and the Co-Issuers.

IN WITNESS WHEREOF, the parties hereto have caused this First Supplemental Indenture to be duly executed and attested, all as of the date first above written.

Exhibit 4.2

SECOND SUPPLEMENTAL INDENTURE (this “Second Supplemental Indenture” ), dated as of February 20, 2014, among Navios Maritime Acquisition Corporation, a Marshall Islands corporation, (the “Company” ), Navios Acquisition Finance (US) Inc., a Delaware corporation (together with the Company, the “Co-Issuers” ), and Navios Acquisition Europe Finance Inc. (the “Guaranteeing Subsidiary” ), a Marshall Islands corporation and a direct subsidiary of the Company, the other Guarantors (as defined in the Indenture referred to herein) and Wells Fargo Bank, National Association, as trustee (or its permitted successor) under the Indenture referred to below (the “Trustee” ) and as collateral trustee (or its permitted successor) under the Indenture referred to below (the “Collateral Trustee” ).

WITNESSETH

WHEREAS, the Co-Issuers and the Guarantors have heretofore executed and delivered to the Trustee an indenture (the “Indenture” ), dated as of November 13, 2013 providing for the issuance of 8.125% First Priority Ship Mortgage Notes due 2021 (the “Notes” );

WHEREAS, the Indenture provides that under certain circumstances each Guaranteeing Subsidiary shall execute and deliver to the Trustee a supplemental indenture pursuant to which a Guaranteeing Subsidiary shall unconditionally guarantee all of the Co-Issuers’ obligations under the Notes and the Indenture on the terms and conditions set forth herein (the “Note Guarantee” ); and

WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and deliver this Second Supplemental Indenture.

NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the receipt of which is hereby acknowledged, the Co-Issuers, the Guaranteeing Subsidiary and the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows:

1. CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the meanings assigned to them in the Indenture.

2. AGREEMENT TO GUARANTEE. The Guaranteeing Subsidiary hereby agrees to provide an unconditional Guarantee, on and subject to the terms, conditions and limitations set forth in the Notation of Guarantee and in the Indenture, including, but not limited, to Article Ten thereof.

4. NEW YORK LAW TO GOVERN. THIS SECOND SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK, WITHOUT GIVING EFFECT TO CONFLICTS OF LAW PRINCIPLES TO THE EXTENT THAT THE APPLICATION OF THE LAWS OF ANOTHER JURISDICTION WOULD BE REQUIRED THEREBY.

5. COUNTERPARTS. The parties may sign any number of copies of this Second Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement.

6. EFFECT OF HEADINGS. The Section headings herein are for convenience only and shall not affect the construction hereof.

7. THE TRUSTEE. The Trustee shall not be responsible in any manner whatsoever for or in respect of the validity or sufficiency of this Second Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by the Guaranteeing Subsidiary and the Co-Issuers.

IN WITNESS WHEREOF, the parties hereto have caused this Second Supplemental Indenture to be duly executed and attested, all as of the date first above written.

[Signature Page to Second Supplemental Indenture]

[Signature Page to Second Supplemental Indenture]

[Signature Page to Second Supplemental Indenture]

Exhibit 4.3

EXECUTION VERSION

THIRD SUPPLEMENTAL INDENTURE (this “Third Supplemental Indenture” ), dated as of March 31, 2014, among Navios Maritime Acquisition Corporation, a Marshall Islands corporation, (the “ Company ”), Navios Acquisition Finance (US) Inc., a Delaware corporation (together with the Company, the “ Co-Issuers ”), the Guarantors (as defined in the Indenture referred to herein) and Wells Fargo Bank, National Association, as trustee (or its permitted successor) under the Indenture referred to below (the “Trustee” ) and as collateral trustee (or its permitted successor) under the Indenture referred to below (the “Collateral Trustee” ).

WITNESSETH

WHEREAS, the Co-Issuers and the Guarantors have heretofore executed and delivered to the Trustee that certain indenture (as amended and supplemented, the “Indenture” ), dated as of November 13, 2013 providing for the issuance of 8.125% First Priority Ship Mortgage Notes due 2021 (the “ Notes ”);

WHEREAS, Section 9.01(7) of the Indenture provides, among other things, that the Co-Issuers, the Guarantors, the Trustee and the Collateral Trustee, as applicable, may amend, waive, supplement or otherwise modify the Indenture, the Notes, the Note Guarantees, any Security Document or any other agreement or instrument entered into in connection with the Indenture without notice to or consent of any Holder of a Note to provide for the issuance of Additional Notes in accordance with the terms of the Indenture; and

WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee and the Collateral Trustee are authorized to execute and deliver this Third Supplemental Indenture.

NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the receipt of which is hereby acknowledged, the Co-Issuers, the Guarantors, the Trustee and the Collateral Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows:

1. CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the meanings assigned to them in the Indenture.

2. ADDITIONAL NOTES. On or after the date hereof, the Co-Issuers shall issue $60,000,000 in aggregate principal amount of Additional Notes which shall be considered Notes for all purposes under the Indenture. The Additional Notes and the Trustee’s certificate of authentication shall be substantially in the form included in the Indenture. For the avoidance of doubt, it is hereby confirmed and acknowledged that the Parallel Debt (as defined in Section 11.13 of the Indenture) includes an amount equal to any and all sums of money from time to time due by the Co-Issuers or any Guarantor in accordance with the terms of the Additional Notes.

3. RATIFICATION. Except as expressly amended and supplemented by this Third Supplemental Indenture, each provision of the Indenture (including any pledge or grant of security interests, mortgages or other liens on the Co-Issuers’ and Guarantors’ assets, including, without limitation, the grant of the security interest and lien on the Co-Issuers in all of their right, title and interest in the Collateral, as security for the obligations under the Indenture and the Notes as described therein) shall remain in full force and effect, and the Indenture is in all respects agreed to, ratified and confirmed by each of the Co-Issuers, the Guarantors, the Trustee, Collateral Agent, Registrar and Paying Agent.

4. NEW YORK LAW TO GOVERN. THIS THIRD SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK, WITHOUT GIVING EFFECT TO CONFLICTS OF LAW PRINCIPLES TO THE EXTENT THAT THE APPLICATION OF THE LAWS OF ANOTHER JURISDICTION WOULD BE REQUIRED THEREBY.

5. COUNTERPARTS. The parties may sign any number of copies of this Third Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement.

6. EFFECT OF HEADINGS. The Section headings herein are for convenience only and shall not affect the construction hereof.

7. THE TRUSTEE. The Trustee shall not be responsible in any manner whatsoever for or in respect of the validity or sufficiency of this Third Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by the Guarantors and the Co-Issuers.

IN WITNESS WHEREOF, the parties hereto have caused this Third Supplemental Indenture to be duly executed and attested, all as of the date first above written.

[Signature Page to Supplemental Indenture]

[Signature Page to Supplemental Indenture]

[Signature Page to Supplemental Indenture]

[Signature Page to the Supplemental Indenture]