<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2013-04-29</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001389545</issuerCik>
        <issuerName>NovaBay Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>NBY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001565534</rptOwnerCik>
            <rptOwnerName>Li Xinzhou</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>NO. 1000, WANGQIAO ROAD,</rptOwnerStreet1>
            <rptOwnerStreet2>PUDONG AREA</rptOwnerStreet2>
            <rptOwnerCity>SHANGHAI</rptOwnerCity>
            <rptOwnerState>F4</rptOwnerState>
            <rptOwnerZipCode>201201</rptOwnerZipCode>
            <rptOwnerStateDescription>CHINA</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2013-04-29</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1743</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2001743</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Pioneer Pharma (Singapore) Pte. Ltd.</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The shares were issued pursuant to an International Distribution Agreement dated as of September 13, 2012, between the Issuer and an affiliate of Pioneer Pharma (Singapore) Pte. Ltd.</footnote>
        <footnote id="F2">The shares are held by Pioneer Pharma (Singapore) Pte. Ltd., which is a wholly owned subsidiary of Pioneer Pharma Co. Ltd., of which the Reporting Person and his spouse are the sole owners. The Reporting Person's previous Form 3 and Form 4 filings incorrectly stated that Pioneer Pharma (Singapore) Pte. Ltd. was a wholly owned subsidiary of Naqu Area Pioneer Pharma, Co. Ltd.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Xinzhou Li</signatureName>
        <signatureDate>2013-11-27</signatureDate>
    </ownerSignature>
</ownershipDocument>
