diff --git a/CHANGES b/CHANGES
index 8f78431b0..c2eb05bc7 100644
--- a/CHANGES
+++ b/CHANGES
@@ -68,7 +68,10 @@ Deprecated
 * ``sphinx.ext.autosummary.Autosummary.warnings``
 * ``sphinx.ext.autosummary.Autosummary.result``
 * ``sphinx.ext.doctest.doctest_encode()``
+* ``sphinx.io.SphinxBaseFileInput``
+* ``sphinx.io.SphinxFileInput.supported``
 * ``sphinx.io.SphinxRSTFileInput``
+* ``sphinx.registry.SphinxComponentRegistry.add_source_input()``
 * ``sphinx.testing.util.remove_unicode_literal()``
 * ``sphinx.util.attrdict``
 * ``sphinx.util.force_decode()``
diff --git a/doc/extdev/index.rst b/doc/extdev/index.rst
index 65031712a..2bfa1bb1c 100644
--- a/doc/extdev/index.rst
+++ b/doc/extdev/index.rst
@@ -278,11 +278,26 @@ The following is a list of deprecated interfaces.
      - 3.0
      - N/A
 
+   * - ``sphinx.io.SphinxBaseFileInput``
+     - 2.0
+     - 3.0
+     - N/A
+
+   * - ``sphinx.io.SphinxFileInput.supported``
+     - 2.0
+     - 3.0
+     - N/A
+
    * - ``sphinx.io.SphinxRSTFileInput``
      - 2.0
      - 3.0
      - N/A
 
+   * - ``sphinx.registry.SphinxComponentRegistry.add_source_input()``
+     - 2.0
+     - 3.0
+     - N/A
+
    * - ``sphinx.writers.latex.LaTeXTranslator._make_visit_admonition()``
      - 2.0
      - 3.0
diff --git a/sphinx/application.py b/sphinx/application.py
index 37f9e600d..0e3bcac3e 100644
--- a/sphinx/application.py
+++ b/sphinx/application.py
@@ -92,7 +92,6 @@ builtin_extensions = (
     'sphinx.directives.other',
     'sphinx.directives.patches',
     'sphinx.extension',
-    'sphinx.io',
     'sphinx.parsers',
     'sphinx.registry',
     'sphinx.roles',
diff --git a/sphinx/io.py b/sphinx/io.py
index 68ebe2b3c..ee4891a2b 100644
--- a/sphinx/io.py
+++ b/sphinx/io.py
@@ -185,21 +185,25 @@ class SphinxBaseFileInput(FileInput):
         self.app = app
         self.env = env
 
+        warnings.warn('%s is deprecated.' % self.__class__.__name__,
+                      RemovedInSphinx30Warning, stacklevel=2)
+
         kwds['error_handler'] = 'sphinx'  # py3: handle error on open.
         super().__init__(*args, **kwds)
 
     def warn_and_replace(self, error):
         # type: (Any) -> Tuple
-        warnings.warn('SphinxBaseFileInput.warn_and_replace() is deprecated. '
-                      'Use UnicodeDecodeErrorHandler instead.',
-                      RemovedInSphinx30Warning, stacklevel=2)
-
         return UnicodeDecodeErrorHandler(self.env.docname)(error)
 
 
-class SphinxFileInput(SphinxBaseFileInput):
+class SphinxFileInput(FileInput):
     """A basic FileInput for Sphinx."""
-    supported = ('*',)  # special source input
+    supported = ('*',)  # RemovedInSphinx30Warning
+
+    def __init__(self, *args, **kwargs):
+        # type: (Any, Any) -> None
+        kwargs['error_handler'] = 'sphinx'
+        super(SphinxFileInput, self).__init__(*args, **kwargs)
 
 
 class SphinxRSTFileInput(SphinxBaseFileInput):
@@ -241,9 +245,6 @@ class SphinxRSTFileInput(SphinxBaseFileInput):
 
     def read(self):  # type: ignore
         # type: () -> StringList
-        warnings.warn('SphinxRSTFileInput is deprecated.',
-                      RemovedInSphinx30Warning, stacklevel=2)
-
         inputstring = super().read()
         lines = string2lines(inputstring, convert_whitespace=True)
         content = StringList()
@@ -287,11 +288,8 @@ def read_doc(app, env, filename):
     error_handler = UnicodeDecodeErrorHandler(env.docname)
     codecs.register_error('sphinx', error_handler)  # type: ignore
 
-    filetype = get_filetype(app.config.source_suffix, filename)
-    input_class = app.registry.get_source_input(filetype)
     reader = SphinxStandaloneReader(app)
-    source = input_class(app, env, source=None, source_path=filename,  # type: ignore
-                         encoding=env.config.source_encoding)
+    filetype = get_filetype(app.config.source_suffix, filename)
     parser = app.registry.create_source_parser(app, filetype)
     if parser.__class__.__name__ == 'CommonMarkParser' and parser.settings_spec == ():
         # a workaround for recommonmark
@@ -301,23 +299,26 @@ def read_doc(app, env, filename):
         #   CommonMarkParser.
         parser.settings_spec = RSTParser.settings_spec
 
-    pub = Publisher(reader=reader,  # type: ignore
-                    parser=parser,
-                    writer=SphinxDummyWriter(),
-                    source_class=SphinxDummySourceClass,
-                    destination=NullOutput())
-    pub.process_programmatic_settings(None, env.settings, None)
-    pub.set_source(source, filename)
+    input_class = app.registry.get_source_input(filetype)
+    if input_class:
+        # Sphinx-1.8 style
+        source = input_class(app, env, source=None, source_path=filename,  # type: ignore
+                             encoding=env.config.source_encoding)
+        pub = Publisher(reader=reader,  # type: ignore
+                        parser=parser,
+                        writer=SphinxDummyWriter(),
+                        source_class=SphinxDummySourceClass,
+                        destination=NullOutput())
+        pub.process_programmatic_settings(None, env.settings, None)
+        pub.set_source(source, filename)
+    else:
+        # Sphinx-2.0 style
+        pub = Publisher(reader=reader,
+                        parser=parser,
+                        writer=SphinxDummyWriter(),
+                        source_class=SphinxFileInput)
+        pub.process_programmatic_settings(None, env.settings, None)
+        pub.set_source(source_path=filename)
+
     pub.publish()
     return pub.document
-
-
-def setup(app):
-    # type: (Sphinx) -> Dict[str, Any]
-    app.registry.add_source_input(SphinxFileInput)
-
-    return {
-        'version': 'builtin',
-        'parallel_read_safe': True,
-        'parallel_write_safe': True,
-    }
diff --git a/sphinx/registry.py b/sphinx/registry.py
index 0090d39a9..311270ccb 100644
--- a/sphinx/registry.py
+++ b/sphinx/registry.py
@@ -337,6 +337,8 @@ class SphinxComponentRegistry:
 
     def add_source_input(self, input_class, override=False):
         # type: (Type[SphinxFileInput], bool) -> None
+        warnings.warn('registry.source_input() is deprecated.',
+                      RemovedInSphinx30Warning, stacklevel=2)
         for filetype in input_class.supported:
             if filetype in self.source_inputs and not override:
                 raise ExtensionError(__('source_input for %r is already registered') %
@@ -352,7 +354,7 @@ class SphinxComponentRegistry:
                 # use special source_input for unknown filetype
                 return self.source_inputs['*']
             except KeyError:
-                raise SphinxError(__('source_input for %s not registered') % filetype)
+                return None
 
     def add_translator(self, name, translator, override=False):
         # type: (str, Type[nodes.NodeVisitor], bool) -> None