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

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2025 Workiva-->
<!--r:50c7771c-6226-48d4-a4a5-d7db3e8ed9b9,g:6875a489-59bc-40fb-ab9d-2f05b82afa6b-->
<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-20250731.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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CoverAbstract"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentType_00707d82-8426-4124-ab76-8a3cf931c624" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_DocumentType_00707d82-8426-4124-ab76-8a3cf931c624" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_DocumentPeriodEndDate_3ef1b6e8-7dac-42ff-971a-9f6c5b78b3a5" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_DocumentPeriodEndDate_3ef1b6e8-7dac-42ff-971a-9f6c5b78b3a5" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityRegistrantName_5d380013-17ed-4ca1-8bf0-de3f9ef00ae9" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityRegistrantName_5d380013-17ed-4ca1-8bf0-de3f9ef00ae9" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityIncorporationStateCountryCode_f9ace418-a9b7-460d-88d9-b3ccf2ff78c6" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityIncorporationStateCountryCode_f9ace418-a9b7-460d-88d9-b3ccf2ff78c6" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityFileNumber_b437762b-6240-4d51-bdc1-83ad738dc3ff" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityFileNumber_b437762b-6240-4d51-bdc1-83ad738dc3ff" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityTaxIdentificationNumber_bd1494a9-cb94-425b-8600-20dbc8a9cf90" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityTaxIdentificationNumber_bd1494a9-cb94-425b-8600-20dbc8a9cf90" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressAddressLine1_cbe4625f-6022-4474-9a6b-7499e69757f8" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityAddressAddressLine1_cbe4625f-6022-4474-9a6b-7499e69757f8" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressCityOrTown_bfc9110d-036d-4863-b5aa-df612b711656" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityAddressCityOrTown_bfc9110d-036d-4863-b5aa-df612b711656" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressStateOrProvince_98649576-50a9-49ca-8550-75c0c7a68374" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityAddressStateOrProvince_98649576-50a9-49ca-8550-75c0c7a68374" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityAddressPostalZipCode_d02c103b-4811-4b3b-8b8f-2642bea62722" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityAddressPostalZipCode_d02c103b-4811-4b3b-8b8f-2642bea62722" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_CityAreaCode_987ec8f9-6ac7-4cbb-8dd8-d24744961c0f" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_CityAreaCode_987ec8f9-6ac7-4cbb-8dd8-d24744961c0f" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_LocalPhoneNumber_8e729ded-a7c7-4eea-87c7-043bec053aa2" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_LocalPhoneNumber_8e729ded-a7c7-4eea-87c7-043bec053aa2" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_WrittenCommunications_0fc69133-c006-4b9d-bb5a-531dfa29f19b" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_WrittenCommunications_0fc69133-c006-4b9d-bb5a-531dfa29f19b" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SolicitingMaterial_66b6f75e-40c8-4aef-8011-73f604aa22ce" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_SolicitingMaterial_66b6f75e-40c8-4aef-8011-73f604aa22ce" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementTenderOffer_85f8a86f-9a69-4d2a-9fd9-c4d54e90037f" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_PreCommencementTenderOffer_85f8a86f-9a69-4d2a-9fd9-c4d54e90037f" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_PreCommencementIssuerTenderOffer_40d01de1-2673-4639-b557-98a14243ce8f" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_PreCommencementIssuerTenderOffer_40d01de1-2673-4639-b557-98a14243ce8f" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_Security12bTitle_91b813e2-e5c0-4c8e-89a7-41e2e9a6f022" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_Security12bTitle_91b813e2-e5c0-4c8e-89a7-41e2e9a6f022" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_TradingSymbol_56804199-7467-4dbf-9def-53c83168cdca" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_TradingSymbol_56804199-7467-4dbf-9def-53c83168cdca" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_SecurityExchangeName_cda8f7c0-df3c-41f9-8f42-69b18bf71317" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_SecurityExchangeName_cda8f7c0-df3c-41f9-8f42-69b18bf71317" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityEmergingGrowthCompany_34175d69-c4ff-448d-8fca-0bfe11881e27" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityEmergingGrowthCompany_34175d69-c4ff-448d-8fca-0bfe11881e27" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityExTransitionPeriod_91bf74d6-ddf8-4cba-a01e-c733c8608118" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityExTransitionPeriod_91bf74d6-ddf8-4cba-a01e-c733c8608118" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_EntityCentralIndexKey_7cf0d7f9-a658-474d-817e-f82637211a6a" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_EntityCentralIndexKey_7cf0d7f9-a658-474d-817e-f82637211a6a" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:loc xlink:type="locator" xlink:label="loc_dei_AmendmentFlag_17124605-ceb5-46b3-8e64-abc984204eb4" 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_c86f97cb-a2e0-4ae5-a4f9-2789ca348396" xlink:to="loc_dei_AmendmentFlag_17124605-ceb5-46b3-8e64-abc984204eb4" xlink:type="arc" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
</link:linkbase>
