diff --git a/include/seqan3/argument_parser/argument_parser.hpp b/include/seqan3/argument_parser/argument_parser.hpp
index 66681dfa39..8399218520 100644
--- a/include/seqan3/argument_parser/argument_parser.hpp
+++ b/include/seqan3/argument_parser/argument_parser.hpp
@@ -28,6 +28,8 @@
 #include <seqan3/core/debug_stream/detail/to_string.hpp>
 #include <seqan3/core/detail/test_accessor.hpp>
 
+SEQAN3_DEPRECATED_HEADER("This header and its functionality is deprecated and will be removed in a future version of SeqAn. Please use the sharg-parser (url: https://github.com/seqan/sharg-parser) instead.");
+
 namespace seqan3
 {
 
diff --git a/include/seqan3/argument_parser/auxiliary.hpp b/include/seqan3/argument_parser/auxiliary.hpp
index 1197f8cd42..e75991f88e 100644
--- a/include/seqan3/argument_parser/auxiliary.hpp
+++ b/include/seqan3/argument_parser/auxiliary.hpp
@@ -19,6 +19,8 @@
 #include <seqan3/core/detail/customisation_point.hpp>
 #include <seqan3/io/stream/concept.hpp>
 
+SEQAN3_DEPRECATED_HEADER("This header and its functionality is deprecated and will be removed in a future version of SeqAn. Please use the sharg-parser (url: https://github.com/seqan/sharg-parser) instead.");
+
 namespace seqan3::custom
 {
 
diff --git a/include/seqan3/argument_parser/exceptions.hpp b/include/seqan3/argument_parser/exceptions.hpp
index e18f91ae59..0493a375c8 100644
--- a/include/seqan3/argument_parser/exceptions.hpp
+++ b/include/seqan3/argument_parser/exceptions.hpp
@@ -13,6 +13,8 @@
 
 #include <seqan3/core/platform.hpp>
 
+SEQAN3_DEPRECATED_HEADER("This header and its functionality is deprecated and will be removed in a future version of SeqAn. Please use the sharg-parser (url: https://github.com/seqan/sharg-parser) instead.");
+
 namespace seqan3
 {
 /*!\brief Argument parser exception that is thrown whenever there is an error
diff --git a/include/seqan3/argument_parser/validators.hpp b/include/seqan3/argument_parser/validators.hpp
index 68f873533c..0484a3601b 100644
--- a/include/seqan3/argument_parser/validators.hpp
+++ b/include/seqan3/argument_parser/validators.hpp
@@ -29,6 +29,8 @@
 #include <seqan3/utility/type_traits/basic.hpp>
 #include <seqan3/utility/views/join_with.hpp>
 
+SEQAN3_DEPRECATED_HEADER("This header and its functionality is deprecated and will be removed in a future version of SeqAn. Please use the sharg-parser (url: https://github.com/seqan/sharg-parser) instead.");
+
 namespace seqan3
 {
 
diff --git a/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp b/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
index 5b71502a8c..b024bbb413 100644
--- a/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
+++ b/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
@@ -16,6 +16,8 @@
 #include <seqan3/core/concept/cereal.hpp>
 #include <seqan3/core/detail/strong_type.hpp>
 
+SEQAN3_DEPRECATED_HEADER("This header and its functionality is deprecated and will be removed in a future version of SeqAn. Please use the hibf-library (url: https://github.com/seqan/hibf) instead.");
+
 namespace seqan3
 {
 //!\brief Determines if the Interleaved Bloom Filter is compressed.
diff --git a/test/documentation/seqan3_doxygen_cfg.in b/test/documentation/seqan3_doxygen_cfg.in
index ca8c6b21c6..645c89651c 100644
--- a/test/documentation/seqan3_doxygen_cfg.in
+++ b/test/documentation/seqan3_doxygen_cfg.in
@@ -352,7 +352,8 @@ PREDEFINED             = CEREAL_SERIALIZE_FUNCTION_NAME=serialize \
                          CEREAL_SAVE_MINIMAL_FUNCTION_NAME=save_minimal \
                          "SEQAN3_DOXYGEN_ONLY(x)= x" \
                          ${SEQAN3_DOXYGEN_PREDEFINED_NDEBUG} \
-                         SEQAN3_WORKAROUND_LITERAL=constexpr
+                         SEQAN3_WORKAROUND_LITERAL=constexpr \
+                         SEQAN3_DEPRECATED_HEADER(x)=
 EXPAND_AS_DEFINED      = SEQAN3_CPO_OVERLOAD_BODY \
                          SEQAN3_CPO_OVERLOAD
 SKIP_FUNCTION_MACROS   = NO
diff --git a/test/seqan3-test.cmake b/test/seqan3-test.cmake
index c6f157d42f..eb1c83f60e 100644
--- a/test/seqan3-test.cmake
+++ b/test/seqan3-test.cmake
@@ -106,6 +106,9 @@ if (NOT TARGET seqan3::test)
     add_library (seqan3_test INTERFACE)
     target_compile_options (seqan3_test INTERFACE "-pedantic" "-Wall" "-Wextra")
 
+    #!TODO remove after release 3.4.0
+    target_compile_definitions (seqan3_test INTERFACE -DSEQAN3_DISABLE_DEPRECATED_WARNINGS)
+
     if (SEQAN3_WITH_WERROR)
         target_compile_options (seqan3_test INTERFACE "-Werror")
         message (STATUS "Building tests with -Werror.")