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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-05-09</periodOfReport>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001188738</rptOwnerCik>
            <rptOwnerName>SIECZKAREK MARK M</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O NOVABAY PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>5980 HORTON STREET, SUITE 550</rptOwnerStreet2>
            <rptOwnerCity>EMERYVILLE</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94608</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.91</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-05-09</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>130890</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2016-05-09</value>
            </exerciseDate>
            <expirationDate>
                <value>2020-05-05</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>130890</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>142557</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Warrant acquisition pursuant to a securities purchase agreement, which is one of a series of securities purchase agreements that the company entered into for the sale of an aggregate of 2,039,530 warrants to 9 accredited investors. The company expects to sell another 1,047,121 warrants pursuant to those same agreements on July 31, 2016.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Justin Hall as attorney in fact for Mark Seiczkarek</signatureName>
        <signatureDate>2016-05-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
