diff --git a/CMakeBuildOptions.cmake b/CMakeBuildOptions.cmake
index 4a4472d678d..fbebbe3ceee 100644
--- a/CMakeBuildOptions.cmake
+++ b/CMakeBuildOptions.cmake
@@ -36,6 +36,7 @@ option (HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place
 mark_as_advanced (HDF5_ENABLE_PREADWRITE)
 
 option (HDF5_ENABLE_DEPRECATED_SYMBOLS "Enable deprecated public API symbols" ON)
+mark_as_advanced (HDF5_ENABLE_DEPRECATED_SYMBOLS)
 
 option (HDF5_MINGW_STATIC_GCC_LIBS "Statically link libgcc/libstdc++" OFF)
 mark_as_advanced (HDF5_MINGW_STATIC_GCC_LIBS)
@@ -78,6 +79,7 @@ mark_as_advanced (HDF5_BUILD_PARALLEL_TOOLS)
 option (HDF5_BUILD_TOOLS "Build HDF5 Tools" ON)
 
 option (HDF5_ENABLE_PLUGIN_SUPPORT "Enable PLUGIN Filters" OFF)
+mark_as_advanced (HDF5_ENABLE_PLUGIN_SUPPORT)
 
 option (HDF5_BUILD_HL_LIB "Build HIGH Level HDF5 Library" ON)
 
diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
index 29bf84d3c84..2cc87e16a27 100644
--- a/CMakeInstallation.cmake
+++ b/CMakeInstallation.cmake
@@ -40,10 +40,12 @@ include (CMakePackageConfigHelpers)
 if (WIN32)
   set (PF_ENV_EXT "(x86)")
   find_program (NSIS_EXECUTABLE NSIS.exe PATHS "$ENV{ProgramFiles}\\NSIS" "$ENV{ProgramFiles${PF_ENV_EXT}}\\NSIS")
+  mark_as_advanced (NSIS_EXECUTABLE)
   if(NOT CPACK_WIX_ROOT)
     file(TO_CMAKE_PATH "$ENV{WIX}" CPACK_WIX_ROOT)
   endif ()
   find_program (WIX_EXECUTABLE candle  PATHS "${CPACK_WIX_ROOT}/bin")
+  mark_as_advanced (WIX_EXECUTABLE)
 endif ()
 
 
@@ -206,6 +208,7 @@ install (
 # Configure the HDF5_Examples.cmake file and the examples
 #-----------------------------------------------------------------------------
 option (HDF5_PACK_EXAMPLES  "Package the HDF5 Library Examples Compressed File" OFF)
+mark_as_advanced (HDF5_PACK_EXAMPLES)
 if (HDF5_PACK_EXAMPLES)
   if (DEFINED CMAKE_TOOLCHAIN_FILE)
     get_filename_component(TOOLCHAIN ${CMAKE_TOOLCHAIN_FILE} NAME)
@@ -476,6 +479,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
     set (CPACK_COMPONENTS_ALL_IN_ONE_PACKAGE ON)
 
     find_program (DPKGSHLIB_EXE dpkg-shlibdeps)
+    mark_as_advanced (DPKGSHLIB_EXE)
     if (DPKGSHLIB_EXE)
       list (APPEND CPACK_GENERATOR "DEB")
       set (CPACK_DEBIAN_PACKAGE_SECTION "Libraries")
@@ -483,6 +487,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
     endif ()
 
     find_program (RPMBUILD_EXE rpmbuild)
+    mark_as_advanced (RPMBUILD_EXE)
     if (RPMBUILD_EXE AND NOT HDF5_ENABLE_PARALLEL)
       list (APPEND CPACK_GENERATOR "RPM")
       set (CPACK_RPM_PACKAGE_RELEASE "1")
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 13c4c0a4bc4..dea8830204b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1101,6 +1101,7 @@ else ()
   set (_HDF5_H5CC_C_COMPILER ${CMAKE_C_COMPILER})
 endif ()
 set (HDF5_H5CC_C_COMPILER ${_HDF5_H5CC_C_COMPILER} CACHE STRING "C compiler to use in h5cc")
+mark_as_advanced (HDF5_H5CC_C_COMPILER)
 
 #-----------------------------------------------------------------------------
 # Java implementation detection for version value
@@ -1471,3 +1472,9 @@ list (REMOVE_DUPLICATES LINK_LIBS_SETTINGS)
 # Installation
 #-----------------------------------------------------------------------------
 include (CMakeInstallation.cmake)
+
+#-----------------------------------------------------------------------------
+# Hide some miscellaneous CMake variables from the default GUI
+#-----------------------------------------------------------------------------
+mark_as_advanced (FETCHCONTENT_BASE_DIR FETCHCONTENT_FULLY_DISCONNECTED FETCHCONTENT_QUIET FETCHCONTENT_UPDATES_DISCONNECTED)
+
diff --git a/CMakeTests.cmake b/CMakeTests.cmake
index 4de4f19d339..0daae663e30 100644
--- a/CMakeTests.cmake
+++ b/CMakeTests.cmake
@@ -106,6 +106,7 @@
   mark_as_advanced (HDF5_TEST_SERIAL)
 
   cmake_dependent_option (HDF5_TEST_TOOLS "Execute tools tests" ON "HDF5_BUILD_TOOLS" OFF)
+  mark_as_advanced (HDF5_TEST_TOOLS)
 
   cmake_dependent_option (HDF5_TEST_EXAMPLES "Execute tests on examples" ON "HDF5_BUILD_EXAMPLES" OFF)
   mark_as_advanced (HDF5_TEST_EXAMPLES)
diff --git a/CTestConfig.cmake b/CTestConfig.cmake
index ec018229b40..06aebda6a74 100644
--- a/CTestConfig.cmake
+++ b/CTestConfig.cmake
@@ -39,6 +39,8 @@ set (CTEST_TEST_TIMEOUT 1200 CACHE STRING
     "Maximum time allowed before CTest will kill the test.")
 set (DART_TESTING_TIMEOUT 1200 CACHE STRING
     "Maximum time allowed before CTest will kill the test." FORCE)
+mark_as_advanced (CTEST_TEST_TIMEOUT)
+mark_as_advanced (DART_TESTING_TIMEOUT)
 
 set (CTEST_SUBMIT_RETRY_DELAY 20 CACHE STRING
     "How long to wait between timed-out CTest submissions.")
diff --git a/HDF5Examples/C/CMakeLists.txt b/HDF5Examples/C/CMakeLists.txt
index 1cb11c73378..527d963dc2a 100644
--- a/HDF5Examples/C/CMakeLists.txt
+++ b/HDF5Examples/C/CMakeLists.txt
@@ -11,7 +11,7 @@ add_subdirectory (${PROJECT_SOURCE_DIR}/H5T)
 
 if (${H5_LIBVER_DIR} GREATER 16)
 #  add_subdirectory (${PROJECT_SOURCE_DIR}/Perf)
-  if (USE_SHARED_LIBS AND H5EXAMPLE_BUILD_FILTERS AND HDF5_PROVIDES_PLUGIN_SUPPORT)
+  if (H5EXAMPLE_USE_SHARED_LIBS AND H5EXAMPLE_BUILD_FILTERS AND HDF5_PROVIDES_PLUGIN_SUPPORT)
     add_subdirectory (${PROJECT_SOURCE_DIR}/H5FLT)
   endif ()
 endif ()
diff --git a/HDF5Examples/CMakeLists.txt b/HDF5Examples/CMakeLists.txt
index cb5086c5ab8..89439f80691 100644
--- a/HDF5Examples/CMakeLists.txt
+++ b/HDF5Examples/CMakeLists.txt
@@ -26,6 +26,7 @@ if (NOT EXAMPLES_EXTERNALLY_CONFIGURED)
   include (TestBigEndian)
   if (NOT WINDOWS)
     TEST_BIG_ENDIAN (H5EXAMPLE_WORDS_BIGENDIAN)
+    mark_as_advanced (H5EXAMPLE_WORDS_BIGENDIAN)
   endif ()
 
   include (${H5EXAMPLE_CONFIG_DIR}/HDFMacros.cmake)
@@ -65,6 +66,7 @@ endif ()
 #-----------------------------------------------------------------------------
 if(NOT DEFINED _h5public_h_contents)
   find_file (_h5public_h H5public.h ${H5EXAMPLE_HDF5_INCLUDE_DIRS})
+  mark_as_advanced (H5EXAMPLE_HDF5_INCLUDE_DIRS)
   file (READ ${_h5public_h} _h5public_h_contents)
 
   string (REGEX REPLACE ".*#define[ \t]+H5_VERS_MAJOR[ \t]+([0-9]*).*$"
diff --git a/HDF5Examples/CMakePresets.json b/HDF5Examples/CMakePresets.json
index 2dade32f482..2bbb18e583a 100644
--- a/HDF5Examples/CMakePresets.json
+++ b/HDF5Examples/CMakePresets.json
@@ -48,7 +48,7 @@
       "inherits": ["ci-base", "ci-base-examples"],
       "cacheVariables": {
         "BUILD_SHARED_LIBS": "ON",
-        "USE_SHARED_LIBS": "ON"
+        "H5EXAMPLE_USE_SHARED_LIBS": "ON"
       }
     },
     {
diff --git a/HDF5Examples/Using_CMake.txt b/HDF5Examples/Using_CMake.txt
index aed87d4e263..b0b81e236be 100644
--- a/HDF5Examples/Using_CMake.txt
+++ b/HDF5Examples/Using_CMake.txt
@@ -253,7 +253,7 @@ III. Defaults in the CMakePresets.json file
 ####      "binaryDir": "${sourceParentDir}/build/${presetName}"
 ####      "name": "ci-StdShar"
 ####        "BUILD_SHARED_LIBS": "ON",
-####        "USE_SHARED_LIBS": "ON"
+####        "H5EXAMPLE_USE_SHARED_LIBS": "ON"
 ####        "CMAKE_BUILD_TYPE": "RelWithDebInfo"
 ####        "H5EXAMPLE_BUILD_FORTRAN": "ON"
 ####        "H5EXAMPLE_BUILD_CXX": "ON"
diff --git a/HDF5Examples/config/HDFMacros.cmake b/HDF5Examples/config/HDFMacros.cmake
index 981f7165035..07a79d6df81 100644
--- a/HDF5Examples/config/HDFMacros.cmake
+++ b/HDF5Examples/config/HDFMacros.cmake
@@ -91,6 +91,7 @@ endmacro ()
 
 macro (HDF_DIR_PATHS package_prefix)
   option (H5EXAMPLE_USE_GNU_DIRS "ON to use GNU Coding Standard install directory variables, OFF to use historical settings" OFF)
+  mark_as_advanced (H5EXAMPLE_USE_GNU_DIRS)
   if (H5EXAMPLE_USE_GNU_DIRS)
     include(GNUInstallDirs)
     if (NOT ${package_prefix}_INSTALL_BIN_DIR)
diff --git a/HDF5Examples/config/cmake/HDFExampleMacros.cmake b/HDF5Examples/config/cmake/HDFExampleMacros.cmake
index 8a9d7ec9c92..68a970d789f 100644
--- a/HDF5Examples/config/cmake/HDFExampleMacros.cmake
+++ b/HDF5Examples/config/cmake/HDFExampleMacros.cmake
@@ -130,10 +130,10 @@ endmacro ()
 
 macro (HDF5_SUPPORT)
   set (CMAKE_MODULE_PATH ${H5EXAMPLE_CONFIG_DIR} ${H5EXAMPLE_RESOURCES_DIR} ${CMAKE_MODULE_PATH})
-  option (USE_SHARED_LIBS "Use Shared Libraries" ON)
+  option (H5EXAMPLE_USE_SHARED_LIBS "Use Shared Libraries" ON)
 
   if (NOT H5EXAMPLE_HDF5_HEADER)
-    if (USE_SHARED_LIBS)
+    if (H5EXAMPLE_USE_SHARED_LIBS)
       set (FIND_HDF_COMPONENTS C shared)
     else ()
       set (FIND_HDF_COMPONENTS C static)
@@ -204,7 +204,7 @@ macro (HDF5_SUPPORT)
         else ()
           add_definitions (-DH5_BUILT_AS_STATIC_LIB)
         endif ()
-        if (USE_SHARED_LIBS AND WIN32)
+        if (H5EXAMPLE_USE_SHARED_LIBS AND WIN32)
           set_property (TARGET ${HDF5_NAMESPACE}h5dump PROPERTY IMPORTED_LOCATION "${HDF5_TOOLS_DIR}/h5dumpdll")
         else ()
           set_property (TARGET ${HDF5_NAMESPACE}h5dump PROPERTY IMPORTED_LOCATION "${HDF5_TOOLS_DIR}/h5dump")
@@ -224,7 +224,7 @@ macro (HDF5_SUPPORT)
         endif ()
         get_filename_component (_LIBRARY_PATH ${HDF5_INCLUDE_DIR} DIRECTORY)
         set (HDF5_LIBRARY_PATH "${_LIBRARY_PATH}/lib")
-        if (USE_SHARED_LIBS AND HDF5_shared_C_FOUND)
+        if (H5EXAMPLE_USE_SHARED_LIBS AND HDF5_shared_C_FOUND)
           set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_C_SHARED_LIBRARY})
         else ()
           set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_C_STATIC_LIBRARY})
@@ -336,7 +336,7 @@ macro (HDF5_SUPPORT)
       #Legacy find_package does not set HDF5_TOOLS_DIR, so we set it here
       set (HDF5_TOOLS_DIR ${HDF5_LIBRARY_DIRS}/../bin)
       #Legacy find_package does not set HDF5_PROVIDES_SHARED_LIBS, so we set it here
-      if (USE_SHARED_LIBS AND EXISTS "${HDF5_LIBRARY_DIRS}/libhdf5.so")
+      if (H5EXAMPLE_USE_SHARED_LIBS AND EXISTS "${HDF5_LIBRARY_DIRS}/libhdf5.so")
         set (HDF5_PROVIDES_SHARED_LIBS 1)
       else ()
         set (HDF5_PROVIDES_SHARED_LIBS 0)
diff --git a/UserMacros.cmake b/UserMacros.cmake
index 822d330f360..4c5e9b3bcc8 100644
--- a/UserMacros.cmake
+++ b/UserMacros.cmake
@@ -24,6 +24,7 @@ endmacro ()
 
 #-------------------------------------------------------------------------------
 option (BUILD_USER_DEFINED_LIBS "Build With User Defined Values" OFF)
+mark_as_advanced (BUILD_USER_DEFINED_LIBS)
 if (BUILD_USER_DEFINED_LIBS)
   MACRO_USER_DEFINED_LIBS ()
 endif ()
diff --git a/config/ConfigureChecks.cmake b/config/ConfigureChecks.cmake
index 8b1d925a2da..9997431cf98 100644
--- a/config/ConfigureChecks.cmake
+++ b/config/ConfigureChecks.cmake
@@ -1021,8 +1021,10 @@ H5ConversionTests (${HDF_PREFIX}_DISABLE_SOME_LDOUBLE_CONV FALSE "Checking IF th
 # Option to enable or disable all non-standard features. Specific features can
 # be enabled or disabled with their respective options below
 option (HDF5_ENABLE_NONSTANDARD_FEATURES "Enable support for non-standard programming language features" ON)
+mark_as_advanced (HDF5_ENABLE_NONSTANDARD_FEATURES)
 # Options for enabling or disabling individual features
 option (HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16 "Enable support for _Float16 C datatype" ON)
+mark_as_advanced (HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16)
 if (NOT HDF5_ENABLE_NONSTANDARD_FEATURES)
   set (HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16 OFF CACHE BOOL "Enable support for _Float16 C datatype" FORCE)
 endif ()
diff --git a/config/HDFMacros.cmake b/config/HDFMacros.cmake
index 53ad04d8366..b015e405a34 100644
--- a/config/HDFMacros.cmake
+++ b/config/HDFMacros.cmake
@@ -46,21 +46,26 @@ macro (SET_HDF_OUTPUT_DIRS package_prefix)
     set (CMAKE_RUNTIME_OUTPUT_DIRECTORY
         ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables."
     )
+    mark_as_advanced (CMAKE_RUNTIME_OUTPUT_DIRECTORY)
     set (CMAKE_LIBRARY_OUTPUT_DIRECTORY
         ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries"
     )
+    mark_as_advanced (CMAKE_LIBRARY_OUTPUT_DIRECTORY)
     set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY
         ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries."
     )
+    mark_as_advanced (CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
     set (CMAKE_Fortran_MODULE_DIRECTORY
         ${PROJECT_BINARY_DIR}/mod CACHE PATH "Single Directory for all fortran modules."
     )
+    mark_as_advanced (CMAKE_Fortran_MODULE_DIRECTORY)
     get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
     if (_isMultiConfig)
       set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF_CFG_NAME})
       set (CMAKE_PDB_OUTPUT_DIRECTORY
           ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files."
       )
+      mark_as_advanced (CMAKE_PDB_OUTPUT_DIRECTORY)
     else ()
       set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
     endif ()
@@ -84,6 +89,7 @@ macro (SET_HDF_OUTPUT_DIRS package_prefix)
       set (CMAKE_GENERIC_PROGRAM_FILES)
     endif ()
     set (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT 0 CACHE PATH "" FORCE)
+    mark_as_advanced (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
   endif ()
 endmacro ()
 
diff --git a/config/cmake/HDF5ExampleCache.cmake b/config/cmake/HDF5ExampleCache.cmake
index 82bbb908631..f60f58422ac 100644
--- a/config/cmake/HDF5ExampleCache.cmake
+++ b/config/cmake/HDF5ExampleCache.cmake
@@ -14,6 +14,7 @@ set (H5EXAMPLE_BUILD_HL ${HDF5_BUILD_HL_LIB} CACHE BOOL "Build High Level exampl
 set (H5EXAMPLE_ENABLE_THREADSAFE ${HDF5_ENABLE_THREADSAFE} CACHE BOOL "Enable examples thread-safety" FORCE)
 set (H5EXAMPLE_ENABLE_PARALLEL ${HDF5_ENABLE_PARALLEL} CACHE BOOL "Enable examples parallel build (requires MPI)" FORCE)
 set (H5EXAMPLE_USE_GNU_DIRS ${HDF5_USE_GNU_DIRS} CACHE BOOL "ON to use GNU Coding Standard install directory variables, OFF to use historical settings" FORCE)
+mark_as_advanced (H5EXAMPLE_USE_GNU_DIRS)
 # set PROVIDES variables for all variables that are used in conditions in HDF5Examples.
 set (HDF5_PROVIDES_FORTRAN ${HDF5_BUILD_FORTRAN} CACHE BOOL "Provides Fortran" FORCE)
 mark_as_advanced (HDF5_PROVIDES_FORTRAN)
@@ -36,10 +37,14 @@ mark_as_advanced (HDF5_PROVIDES_SUBFILING_VFD)
 
 # Preset HDF5 cache vars to this project's libraries instead of searching
 set (H5EXAMPLE_HDF5_HEADER "H5pubconf.h" CACHE STRING "Name of HDF5 header" FORCE)
+mark_as_advanced (H5EXAMPLE_HDF5_HEADER)
 # set (H5EXAMPLE_HDF5_INCLUDE_DIRS $<TARGET_PROPERTY:${HDF5_LIBSH_TARGET},INCLUDE_DIRECTORIES> CACHE PATH "HDF5 include dirs" FORCE)
 set (H5EXAMPLE_HDF5_INCLUDE_DIRS "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR}" CACHE PATH "HDF5 include dirs" FORCE)
+mark_as_advanced (H5EXAMPLE_HDF5_INCLUDE_DIRS)
 set (H5EXAMPLE_HDF5_DIR ${CMAKE_CURRENT_BINARY_DIR} CACHE STRING "HDF5 build folder" FORCE)
+mark_as_advanced (H5EXAMPLE_HDF5_DIR)
 set (EXAMPLES_EXTERNALLY_CONFIGURED ON CACHE BOOL "Examples build is used in another project" FORCE)
+mark_as_advanced (EXAMPLES_EXTERNALLY_CONFIGURED)
 
 # Set up example-specific variables
 set (EXAMPLE_VARNAME "H5")
@@ -66,8 +71,9 @@ message (STATUS "HDF5 H5_LIBVER_DIR: ${H5_LIBVER_DIR} HDF5_API_VERSION: ${HDF5_D
 # Configure linking and include directories based on shared/static build and enabled components
 if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
   # Static build configuration
-  set (USE_SHARED_LIBS OFF CACHE BOOL "Use Shared Libraries for Examples" FORCE)
+  set (H5EXAMPLE_USE_SHARED_LIBS OFF CACHE BOOL "Use Shared Libraries for Examples" FORCE)
   set (H5EXAMPLE_HDF5_LINK_LIBS ${HDF5_LIB_TARGET} CACHE STRING "HDF5 target" FORCE)
+  mark_as_advanced (H5EXAMPLE_HDF5_LINK_LIBS)
   if (HDF5_BUILD_HL_LIB)
     set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_HL_LIB_TARGET})
     set (H5EXAMPLE_HDF5_INCLUDE_DIRS "${H5EXAMPLE_HDF5_INCLUDE_DIRS};${HDF5_HL_SRC_DIR};${HDF5_HL_SRC_BINARY_DIR}" CACHE PATH "HDF5 include dirs" FORCE)
@@ -75,6 +81,7 @@ if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
   if (HDF5_BUILD_FORTRAN)
     set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_F90_LIB_TARGET})
     set (H5EXAMPLE_MOD_EXT "/static" CACHE STRING "Use Static Modules for Examples" FORCE)
+    mark_as_advanced (H5EXAMPLE_MOD_EXT)
     if (HDF5_BUILD_HL_LIB)
       set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_HL_F90_LIB_TARGET})
     endif ()
@@ -88,8 +95,9 @@ if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
   endif ()
 else ()
   # Shared build configuration
-  set (USE_SHARED_LIBS ON CACHE BOOL "Use Shared Libraries for Examples" FORCE)
+  set (H5EXAMPLE_USE_SHARED_LIBS ON CACHE BOOL "Use Shared Libraries for Examples" FORCE)
   set (H5EXAMPLE_HDF5_LINK_LIBS ${HDF5_LIBSH_TARGET} CACHE STRING "HDF5 target" FORCE)
+  mark_as_advanced (H5EXAMPLE_HDF5_LINK_LIBS)
   if (HDF5_BUILD_HL_LIB)
     set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_HL_LIBSH_TARGET})
     set (H5EXAMPLE_HDF5_INCLUDE_DIRS "${H5EXAMPLE_HDF5_INCLUDE_DIRS};${HDF5_HL_SRC_DIR};${HDF5_HL_SRC_BINARY_DIR}" CACHE PATH "HDF5 include dirs" FORCE)
@@ -100,6 +108,7 @@ else ()
   if (HDF5_BUILD_FORTRAN)
     set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_F90_LIBSH_TARGET})
     set (H5EXAMPLE_MOD_EXT "/shared" CACHE STRING "Use Shared Modules for Examples" FORCE)
+    mark_as_advanced (H5EXAMPLE_MOD_EXT)
     if (HDF5_BUILD_HL_LIB)
       set (H5EXAMPLE_HDF5_LINK_LIBS ${H5EXAMPLE_HDF5_LINK_LIBS} ${HDF5_HL_F90_LIBSH_TARGET})
     endif ()
@@ -150,8 +159,12 @@ message (STATUS "HDF5 Example link libs: ${H5EXAMPLE_HDF5_LINK_LIBS} Includes: $
 
 # Set up tool and executable variables for use in example tests
 set (HDF5_TOOLS_DIR ${CMAKE_TEST_OUTPUT_DIRECTORY} CACHE STRING "HDF5 Directory for all Executables" FORCE)
+mark_as_advanced (HDF5_TOOLS_DIR)
 set (H5EXAMPLE_HDF5_DUMP_EXECUTABLE $<TARGET_FILE:h5dump> CACHE STRING "HDF5 h5dump target" FORCE)
+mark_as_advanced (H5EXAMPLE_HDF5_DUMP_EXECUTABLE)
 set (H5EXAMPLE_HDF5_REPACK_EXECUTABLE $<TARGET_FILE:h5repack> CACHE STRING "HDF5 h5repack target" FORCE)
+mark_as_advanced (H5EXAMPLE_HDF5_REPACK_EXECUTABLE)
 set (H5EXAMPLE_WORDS_BIGENDIAN ${H5_WORDS_BIGENDIAN} CACHE BOOL "System is Big Endian" FORCE)
+mark_as_advanced (H5EXAMPLE_WORDS_BIGENDIAN)
 
 # End of HDF5ExampleCache.cmake
diff --git a/config/flags/HDFCompilerCXXFlags.cmake b/config/flags/HDFCompilerCXXFlags.cmake
index e15160815e1..bfc4ba783d8 100644
--- a/config/flags/HDFCompilerCXXFlags.cmake
+++ b/config/flags/HDFCompilerCXXFlags.cmake
@@ -141,6 +141,7 @@ if (CMAKE_CXX_COMPILER_LOADED)
 
   set (_HDF5_H5CC_CXX_COMPILER ${CMAKE_CXX_COMPILER})
   set (HDF5_H5CC_CXX_COMPILER ${_HDF5_H5CC_CXX_COMPILER} CACHE STRING "C++ compiler to use in h5c++")
+  mark_as_advanced (HDF5_H5CC_CXX_COMPILER)
 endif ()
 
 #-----------------------------------------------------------------------------
diff --git a/config/flags/HDFCompilerFlags.cmake b/config/flags/HDFCompilerFlags.cmake
index f299ba7d303..4460e7baf0b 100644
--- a/config/flags/HDFCompilerFlags.cmake
+++ b/config/flags/HDFCompilerFlags.cmake
@@ -32,6 +32,7 @@ endif ()
 # Option to allow the user to disable compiler warnings
 #-----------------------------------------------------------------------------
 option (HDF5_DISABLE_COMPILER_WARNINGS "Disable compiler warnings" OFF)
+mark_as_advanced (HDF5_DISABLE_COMPILER_WARNINGS)
 if (HDF5_DISABLE_COMPILER_WARNINGS)
   message (STATUS "....Compiler warnings are suppressed")
   # MSVC uses /w to suppress warnings.  It also complains if another
@@ -89,6 +90,7 @@ endif ()
 # our control (MPI, HDFS, etc.) can also raise warnings.
 #-----------------------------------------------------------------------------
 option (HDF5_ENABLE_WARNINGS_AS_ERRORS "Interpret some warnings as errors" OFF)
+mark_as_advanced (HDF5_ENABLE_WARNINGS_AS_ERRORS)
 if (HDF5_ENABLE_WARNINGS_AS_ERRORS)
   message (STATUS "...some warnings will be interpreted as errors")
 endif ()
@@ -116,6 +118,7 @@ endif ()
 # Developer warnings (suggestions from gcc, not code problems)
 #-----------------------------------------------------------------------------
 option (HDF5_ENABLE_DEV_WARNINGS "Enable HDF5 developer group warnings" OFF)
+mark_as_advanced (HDF5_ENABLE_DEV_WARNINGS)
 if (${HDF_CFG_NAME} MATCHES "Developer")
   # Developer build modes should always have these types of warnings enabled
   set (HDF5_ENABLE_DEV_WARNINGS ON CACHE BOOL "Enable HDF5 developer group warnings" FORCE)
@@ -145,6 +148,7 @@ endif ()
 # Option to allow the user to enable all warnings
 #-----------------------------------------------------------------------------
 option (HDF5_ENABLE_ALL_WARNINGS "Enable all warnings" ON)
+mark_as_advanced (HDF5_ENABLE_ALL_WARNINGS)
 if (HDF5_ENABLE_ALL_WARNINGS)
   message (STATUS "....All Warnings are enabled")
   if (MSVC)
@@ -172,7 +176,7 @@ if (HDF5_ENABLE_ASSERTS MATCHES "YES")
 elseif (HDF5_ENABLE_ASSERTS MATCHES "NO")
   add_compile_options ("-DNDEBUG")
 endif ()
-MARK_AS_ADVANCED (HDF5_ENABLE_ASSERTS)
+mark_as_advanced (HDF5_ENABLE_ASSERTS)
 
 #-----------------------------------------------------------------------------
 # This option will force/override the default setting for all configurations
@@ -180,7 +184,7 @@ MARK_AS_ADVANCED (HDF5_ENABLE_ASSERTS)
 #option (HDF5_ENABLE_SYMBOLS "Add debug symbols to the library independent of the build mode and optimization level." OFF)
 set (HDF5_ENABLE_SYMBOLS "OFF" CACHE STRING "Add debug symbols to the library independent of the build mode and optimization level (OFF NO YES)")
 set_property (CACHE HDF5_ENABLE_SYMBOLS PROPERTY STRINGS OFF NO YES)
-MARK_AS_ADVANCED (HDF5_ENABLE_SYMBOLS)
+mark_as_advanced (HDF5_ENABLE_SYMBOLS)
 
 #-----------------------------------------------------------------------------
 # This option will force/override the default setting for all configurations
@@ -189,7 +193,7 @@ option (HDF5_ENABLE_PROFILING "Enable profiling flags independently from the bui
 if (HDF5_ENABLE_PROFILING)
   list (APPEND HDF5_CMAKE_C_FLAGS "${PROFILE_CFLAGS}")
 endif ()
-MARK_AS_ADVANCED (HDF5_ENABLE_PROFILING)
+mark_as_advanced (HDF5_ENABLE_PROFILING)
 
 #-----------------------------------------------------------------------------
 # This option will force/override the default setting for all configurations
@@ -198,7 +202,7 @@ option (HDF5_ENABLE_OPTIMIZATION "Enable optimization flags/settings independent
 if (HDF5_ENABLE_OPTIMIZATION)
   list (APPEND HDF5_CMAKE_C_FLAGS "${OPTIMIZE_CFLAGS}")
 endif ()
-MARK_AS_ADVANCED (HDF5_ENABLE_OPTIMIZATION)
+mark_as_advanced (HDF5_ENABLE_OPTIMIZATION)
 
 #-----------------------------------------------------------------------------
 # The build mode flags are not added to CMAKE_C_FLAGS, so create a separate
diff --git a/config/flags/HDFCompilerFortranFlags.cmake b/config/flags/HDFCompilerFortranFlags.cmake
index f5fbfe07b64..85b2a52bb16 100644
--- a/config/flags/HDFCompilerFortranFlags.cmake
+++ b/config/flags/HDFCompilerFortranFlags.cmake
@@ -74,6 +74,7 @@ else ()
   set (_HDF5_H5CC_Fortran_COMPILER ${CMAKE_Fortran_COMPILER})
 endif ()
 set (HDF5_H5CC_Fortran_COMPILER ${_HDF5_H5CC_Fortran_COMPILER} CACHE STRING "Fortran compiler to use in h5fc")
+mark_as_advanced (HDF5_H5CC_Fortran_COMPILER)
 
 #-----------------------------------------------------------------------------
 # The build mode flags are not added to CMAKE_Fortran_FLAGS, so create a separate
diff --git a/hl/CMakeLists.txt b/hl/CMakeLists.txt
index cfd1fab32db..b839c4ad189 100644
--- a/hl/CMakeLists.txt
+++ b/hl/CMakeLists.txt
@@ -5,6 +5,7 @@ project (HDF5_HL C)
 # Option to use new-style references with dimension scale APIs
 #-----------------------------------------------------------------------------
 option (HDF5_DIMENSION_SCALES_NEW_REF  "Use new-style references with dimension scale APIs" OFF)
+mark_as_advanced (HDF5_DIMENSION_SCALES_NEW_REF)
 if (HDF5_DIMENSION_SCALES_NEW_REF)
   set (H5_DIMENSION_SCALES_WITH_NEW_REF 1)
 endif ()
diff --git a/java/CMakeLists.txt b/java/CMakeLists.txt
index a7a3a5b6ab9..7e845943935 100644
--- a/java/CMakeLists.txt
+++ b/java/CMakeLists.txt
@@ -5,6 +5,8 @@ project (HDF5_JAVA C Java)
 # Include some macros for reusable code
 #-----------------------------------------------------------------------------
 include (UseJava)
+mark_as_advanced (CMAKE_Java_ARCHIVE)
+mark_as_advanced (CMAKE_Java_RUNTIME)
 
 if (WIN32)
   set (HDF_JRE_DIRECTORY "C:/Program Files/Java/jre")
@@ -49,6 +51,7 @@ if (Java_VERSION_STRING VERSION_GREATER_EQUAL "25.0.0")
             NO_DEFAULT_PATH
         )
     endif ()
+    mark_as_advanced (JEXTRACT_EXECUTABLE)
 
     if (NOT JEXTRACT_EXECUTABLE)
         message (FATAL_ERROR "Could not find jextract executable. "
@@ -188,6 +191,7 @@ install (
 # Option to include jre
 #-----------------------------------------------------------------------------
 option (HDF5_JAVA_PACK_JRE  "Package a JRE installer directory" OFF)
+mark_as_advanced (HDF5_JAVA_PACK_JRE)
 if (HDF5_JAVA_PACK_JRE)
   install (
       DIRECTORY ${HDF_JRE_DIRECTORY}
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 1b8a2be9d0e..e9a48e044c0 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1188,6 +1188,7 @@ set (H5_PUBLIC_GENERATED_HEADERS
 )
 
 option (HDF5_GENERATE_HEADERS "Rebuild Generated Files" OFF)
+mark_as_advanced (HDF5_GENERATE_HEADERS)
 if (HDF5_GENERATE_HEADERS)
   set_source_files_properties(${H5_GENERATED_HEADERS} PROPERTIES GENERATED TRUE)
   if (H5_PERL_FOUND)
diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake
index 999bc8dc994..e6ddd365770 100644
--- a/test/CMakeTests.cmake
+++ b/test/CMakeTests.cmake
@@ -998,11 +998,13 @@ if (BUILD_SHARED_LIBS)
 endif ()
 
 option (HDF5_TEST_SHELL_SCRIPTS "Enable shell script tests" ON)
+mark_as_advanced (HDF5_TEST_SHELL_SCRIPTS)
 if (HDF5_TEST_SHELL_SCRIPTS)
   include (ShellTests.cmake)
 endif()
 
 option (ENABLE_EXTENDED_TESTS "Enable extended tests" OFF)
+mark_as_advanced (ENABLE_EXTENDED_TESTS)
 if (ENABLE_EXTENDED_TESTS)
 ##############################################################################
 ###    S W M R  T E S T S
diff --git a/test/ShellTests.cmake b/test/ShellTests.cmake
index 2d508e01626..6533c2120ef 100644
--- a/test/ShellTests.cmake
+++ b/test/ShellTests.cmake
@@ -16,6 +16,7 @@
 ##############################################################################
 
 find_program (PWSH NAMES pwsh powershell)
+mark_as_advanced (PWSH)
 if (PWSH)
     file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/H5TEST/use_cases_test")
     file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/H5TEST/swmr_test")
@@ -40,6 +41,7 @@ if (PWSH)
     #)
 elseif (UNIX)
   find_program (SH_PROGRAM bash)
+  mark_as_advanced (SH_PROGRAM)
   if (SH_PROGRAM)
     set (srcdir ${HDF5_TEST_SOURCE_DIR})
     set (H5_UTILS_TEST_BUILDDIR ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})