<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2025 Workiva-->
<!--r:719b80c5-8636-4460-a833-508c0acd1d9b,g:e1e9dd42-6405-4a04-8827-3acbbcc4d3fa-->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.nautilus.bio/role/Cover" xlink:type="simple" xlink:href="naut-20251028.xsd#Cover"/>
  <link:presentationLink xlink:role="http://www.nautilus.bio/role/Cover" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CoverAbstract"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentType_ea968745-73cf-438a-b706-723d0fbdf97d" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentType"/>
    <link:presentationArc order="1" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_DocumentType_ea968745-73cf-438a-b706-723d0fbdf97d" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentPeriodEndDate_1432cfee-d6f4-4cdb-a3e8-50dcb417bbe3" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentPeriodEndDate"/>
    <link:presentationArc order="2" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_DocumentPeriodEndDate_1432cfee-d6f4-4cdb-a3e8-50dcb417bbe3" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityRegistrantName_6b92aa52-2796-4679-82c3-4924982bc5e5" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityRegistrantName"/>
    <link:presentationArc order="3" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityRegistrantName_6b92aa52-2796-4679-82c3-4924982bc5e5" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityIncorporationStateCountryCode_3750f313-6e68-4704-b35c-cd38a35597ed" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityIncorporationStateCountryCode"/>
    <link:presentationArc order="4" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityIncorporationStateCountryCode_3750f313-6e68-4704-b35c-cd38a35597ed" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityFileNumber_0ec26c55-2711-491f-83c2-37e2b3072a44" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityFileNumber"/>
    <link:presentationArc order="5" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityFileNumber_0ec26c55-2711-491f-83c2-37e2b3072a44" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityTaxIdentificationNumber_43e8acc5-f439-408f-9789-84b707fee714" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityTaxIdentificationNumber"/>
    <link:presentationArc order="6" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityTaxIdentificationNumber_43e8acc5-f439-408f-9789-84b707fee714" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressAddressLine1_06e6ec91-9e1b-40f6-85f4-cfa453327d9c" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressAddressLine1"/>
    <link:presentationArc order="7" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityAddressAddressLine1_06e6ec91-9e1b-40f6-85f4-cfa453327d9c" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressCityOrTown_5b829fa5-d96e-485e-b27f-a06c3831b616" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressCityOrTown"/>
    <link:presentationArc order="8" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityAddressCityOrTown_5b829fa5-d96e-485e-b27f-a06c3831b616" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressStateOrProvince_a4f457cc-6461-45d8-8b3c-1076dc2a1958" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressStateOrProvince"/>
    <link:presentationArc order="9" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityAddressStateOrProvince_a4f457cc-6461-45d8-8b3c-1076dc2a1958" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressPostalZipCode_7672a6c6-7434-461f-94b9-70d9a81dd087" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressPostalZipCode"/>
    <link:presentationArc order="10" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityAddressPostalZipCode_7672a6c6-7434-461f-94b9-70d9a81dd087" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_CityAreaCode_cecd7f3b-d08d-423d-89b7-3f02b74cb8a9" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CityAreaCode"/>
    <link:presentationArc order="11" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_CityAreaCode_cecd7f3b-d08d-423d-89b7-3f02b74cb8a9" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_LocalPhoneNumber_2e6bfbb0-a129-4de4-ad46-0ab21c3d0f9f" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_LocalPhoneNumber"/>
    <link:presentationArc order="12" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_LocalPhoneNumber_2e6bfbb0-a129-4de4-ad46-0ab21c3d0f9f" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_WrittenCommunications_7c4c2376-0f56-4e42-b4c5-fbdde010d181" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_WrittenCommunications"/>
    <link:presentationArc order="13" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_WrittenCommunications_7c4c2376-0f56-4e42-b4c5-fbdde010d181" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SolicitingMaterial_5e2569d7-2fef-4a9a-8183-cb6244fa3db8" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_SolicitingMaterial"/>
    <link:presentationArc order="14" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_SolicitingMaterial_5e2569d7-2fef-4a9a-8183-cb6244fa3db8" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementTenderOffer_3aff8631-3858-4794-9cb8-f06d34b6a5bf" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_PreCommencementTenderOffer"/>
    <link:presentationArc order="15" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_PreCommencementTenderOffer_3aff8631-3858-4794-9cb8-f06d34b6a5bf" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementIssuerTenderOffer_7bc84bc3-932e-40b6-b3f7-0f1a5fc714d9" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_PreCommencementIssuerTenderOffer"/>
    <link:presentationArc order="16" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_PreCommencementIssuerTenderOffer_7bc84bc3-932e-40b6-b3f7-0f1a5fc714d9" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_Security12bTitle_ea2d14d5-49d6-4684-8f42-cc8298ae9f32" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_Security12bTitle"/>
    <link:presentationArc order="17" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_Security12bTitle_ea2d14d5-49d6-4684-8f42-cc8298ae9f32" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_TradingSymbol_5b14dfb3-96dd-4d80-8b1a-bc35090e69a4" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_TradingSymbol"/>
    <link:presentationArc order="18" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_TradingSymbol_5b14dfb3-96dd-4d80-8b1a-bc35090e69a4" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SecurityExchangeName_b3c905e9-fbb1-44ef-b465-6e011d7a0a00" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_SecurityExchangeName"/>
    <link:presentationArc order="19" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_SecurityExchangeName_b3c905e9-fbb1-44ef-b465-6e011d7a0a00" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityEmergingGrowthCompany_65eea221-af99-455f-8bbf-b15ae9213420" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityEmergingGrowthCompany"/>
    <link:presentationArc order="20" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityEmergingGrowthCompany_65eea221-af99-455f-8bbf-b15ae9213420" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityExTransitionPeriod_48dff341-d4f8-49ba-af82-ef43a3112333" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityExTransitionPeriod"/>
    <link:presentationArc order="21" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityExTransitionPeriod_48dff341-d4f8-49ba-af82-ef43a3112333" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityCentralIndexKey_8f0c6cd1-dceb-4dcb-b331-7efc828df2a7" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityCentralIndexKey"/>
    <link:presentationArc order="22" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_EntityCentralIndexKey_8f0c6cd1-dceb-4dcb-b331-7efc828df2a7" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_AmendmentFlag_1ce8e6a7-cd86-4330-ba4a-a1a3dcd0a4fa" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AmendmentFlag"/>
    <link:presentationArc order="23" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="loc_dei_CoverAbstract_b7bfbc98-f031-4766-b9f2-b0aad6c382a2" xlink:to="loc_dei_AmendmentFlag_1ce8e6a7-cd86-4330-ba4a-a1a3dcd0a4fa" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
</link:linkbase>
