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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2012-10-29</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001561909</rptOwnerCik>
            <rptOwnerName>NAQU AREA PIONEER PHARMA CO., LTD.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>NO. 1000, WANGQIAO ROAD, PUDONG AREA</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SHANGHAI, P.R. OF CHINA</rptOwnerCity>
            <rptOwnerState></rptOwnerState>
            <rptOwnerZipCode>201201</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isTenPercentOwner>1</isTenPercentOwner>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>800000</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Pioneer Pharma (Singapore) Pte. Ltd. is a 100% wholly-owned subsidiary of Naqu Area Pioneer Pharma C</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant</value>
                <footnoteId id="F3"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.50</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2012-09-13</value>
            </exerciseDate>
            <expirationDate>
                <value>2012-08-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>800000</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Pioneer Pharma (Singapore) Pte. Ltd. is a 100% wholly-owned subsidiary of Naqu Area Pioneer Pharma C</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Reporting owner has an indirect contractual right to acquire common stock (1,200,000)</footnote>
        <footnote id="F2">THe shares are held directly by Pioneer Pharma (Singapore) Pte. Ltd. Pioneer Pharma (Singapore) Pte. Ltd. is a 100% wholly-owned subsidiary of Naqu Area Pioneer Pharma Co. Ltd. and, as a result, Naqu Area Pioneer Pharma Co. Ltd. may be deemed to beneficially own the shares held by Pioneer Pharma (Singapore) Pte. Ltd.</footnote>
        <footnote id="F3">Warrant to purchase Common stock</footnote>
        <footnote id="F4">Reporting owner has an indirect right to acquire Warrants to puchase common stock (1,200,000)</footnote>
        <footnote id="F5">THe warrants are held directly by Pioneer Pharma (Singapore) Pte. Ltd. Pioneer Pharma (Singapore) Pte. Ltd. is a 100% wholly-owned subsidiary of Naqu Area Pioneer Pharma Co. Ltd. and, as a result, Naqu Area Pioneer Pharma Co. Ltd. may be deemed to beneficially own the shares held by Pioneer Pharma (Singapore) Pte. Ltd.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Xinzhou (Paul) Li</signatureName>
        <signatureDate>2012-11-14</signatureDate>
    </ownerSignature>
</ownershipDocument>
