<?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>0001534338</rptOwnerCik>
            <rptOwnerName>Bessemer Venture Partners VII L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001540726</rptOwnerCik>
            <rptOwnerName>Deer VII &amp; Co. Ltd.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001540731</rptOwnerCik>
            <rptOwnerName>Deer VII &amp; Co. L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001459524</rptOwnerCik>
            <rptOwnerName>BVP VII SPECIAL OPPORTUNITY FUND LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001407577</rptOwnerCik>
            <rptOwnerName>Bessemer Venture Partners VII Institutional L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O BESSEMER VENTURE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>1865 PALMER AVENUE, SUITE 104</rptOwnerStreet2>
            <rptOwnerCity>LARCHMONT</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10538</rptOwnerZipCode>
            <rptOwnerStateDescription></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>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>2227365</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2227365</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>36000</value>
                    <footnoteId id="F4"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>14.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2263365</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>6122448</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>1466800</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>3174603</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>760565</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 the total 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">Deer VII &amp; Co. Ltd. (&quot;Deer Ltd.&quot;) is the general partner of Deer VII &amp; Co. L.P. (&quot;Deer L.P.&quot;), which is the general partner of BVP VII Inst, BVP VII and BVP VII SOF. Deer Ltd. and Deer L.P. disclaim beneficial ownership of the securities held by the Funds, and this report shall not be deemed an admission that Deer Ltd. and Deer L.P. are the beneficial owners of such securities, except to the extent of their pecuniary interest therein, if any, by virtue of their direct and indirect general partner interests in the Funds.</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/Scott Ring, General Counsel, Deer VII &amp; Co. Ltd., the General Partner of Deer VII &amp; Co. L.P., the General Partner of Bessemer Venture Partners VII L.P.</signatureName>
        <signatureDate>2017-11-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Scott Ring, General Counsel, Deer VII &amp; Co. Ltd., the General Partner of Deer VII &amp; Co. L.P., the General Partner of Bessemer Venture Partners VII Institutional L.P.</signatureName>
        <signatureDate>2017-11-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Scott Ring, General Counsel, Deer VII &amp; Co. Ltd., the General Partner of Deer VII &amp; Co. L.P., the General Partner of BVP VII Special Opportunity Fund L.P.</signatureName>
        <signatureDate>2017-11-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Scott Ring, General Counsel, Deer VII &amp; Co. Ltd., the General Partner of Deer VII &amp; Co. L.P</signatureName>
        <signatureDate>2017-11-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/Scott Ring, General Counsel, Deer VII &amp; Co. Ltd</signatureName>
        <signatureDate>2017-11-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
