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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2017-11-06</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001624658</issuerCik>
        <issuerName>Allena Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>ALNA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001362099</rptOwnerCik>
            <rptOwnerName>Kraus Stephen</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ALLENA PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>ONE NEWTON EXECUTIVE PARK, SUITE 202</rptOwnerStreet2>
            <rptOwnerCity>NEWTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02459</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2017-11-06</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>0</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2017-11-06</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>0</value>
                    <footnoteId id="F4"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                    <footnoteId id="F4"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-11-06</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>0</value>
                    <footnoteId id="F5"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>0</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Series B Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-11-06</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>0</value>
                    <footnoteId id="F7"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>0</value>
                    <footnoteId id="F8"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F7"/>
                    <footnoteId id="F8"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Represents an aggregate of 2,227,365 shares received by Bessemer Venture Partners VII Institutional L.P. (&quot;BVP VII Inst&quot;), Bessemer Venture Partners VII, L.P. (&quot;BVP VII&quot;) and BVP VII Special Opportunity Fund L.P. (&quot;BVP VII SOF&quot; and together with BVP VII Inst and BVP VII, collectively, the &quot;Funds&quot;) upon conversion of the Series A Preferred Stock and Series B Preferred Stock upon closing of the Issuer's initial public offering.  Following the reported transaction, BVP VII Inst, BVP VII and BVP VII SOF owned 311,829 shares, 712,757 shares and 1,202,779 shares of Common Stock, respectively.</footnote>
        <footnote id="F2">The Series A Preferred Stock and Series B Preferred Stock converted into Common Stock on a 4.174-for-one basis upon the closing of the Issuer's initial public offering without payment of consideration. The Series A Preferred Stock and B Preferred Stock were convertible at any time at the holder's election and automatically upon the closing of the Issuer's initial public offering. The Preferred Stock had no expiration date.</footnote>
        <footnote id="F3">The Reporting Person has a passive economic interest in the shares held by the Funds through an interest in (1) BVP VII and (2) Deer VII &amp; Co. L.P. (&quot;Deer L.P.&quot;), the general partner of each of the Funds. The Reporting Person disclaims beneficial ownership of the securities held by the Funds, except to the extent of his pecuniary interest, if any, in such securities by virtue of his interest in Deer L.P. and his indirect limited partnership interest in BVP VII. This report shall not be deemed an admission that the Reporting Person is the beneficial owner of such securities.</footnote>
        <footnote id="F4">On November 6, 2017, BVP VII Inst, BVP VII and BVP VII SOF purchased 5,040 shares, 11,520 shares and 19,440 shares of Common Stock, respectively, at a price per share of $14.00 in the Issuer's initial public offering.  Following the reported transaction, BVP VII Inst, BVP VII and BVP VII SOF owned 316,869 shares, 724,277 shares and 1,222,219 shares of Common Stock, respectively.</footnote>
        <footnote id="F5">Prior to the conversion, BVP VII Inst, BVP VII and BVP VII SOF owned 857,143 shares, 1,959,184 shares and 3,306,121 shares of Series A Preferred Stock, respectively.</footnote>
        <footnote id="F6">Prior to the conversion, BVP VII Inst, BVP VII and BVP VII SOF owned 205,350 shares, 469,376 shares, and 792,074 shares, respectively, of Common Stock issuable upon conversion of the Series A Preferred Stock.</footnote>
        <footnote id="F7">Prior to the conversion, BVP VII Inst, BVP VII and BVP VII SOF owned 444,444 shares, 1,015,873 shares and 1,714,286 shares of Series B Preferred Stock, respectively.</footnote>
        <footnote id="F8">Prior to the conversion, BVP VII Inst, BVP VII, and BVP VII SOF owned 106,479 shares, 243,381 shares, and, 410,705 shares, respectively, of Common Stock issuable upon conversion of the Series B Preferred Stock.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Kevin Brennan, attorney in fact</signatureName>
        <signatureDate>2017-11-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
