diff --git a/doc/sphinx/cti/phases.rst b/doc/sphinx/cti/phases.rst
index d831c7624..fd8d4d7c4 100644
--- a/doc/sphinx/cti/phases.rst
+++ b/doc/sphinx/cti/phases.rst
@@ -109,6 +109,8 @@ to synchronize the elements among multiple phases, so that each phase contains
 the same elements with the same ordering. In such cases, simply use the same
 string in the elements field for all phases.
 
+.. _sec-defining-species:
+
 Defining the Species
 ^^^^^^^^^^^^^^^^^^^^
 
@@ -160,6 +162,8 @@ definitions with imported ones, by specifying a sequence of strings::
 Note that the strings must be separated by commas, and enclosed in square
 brackets or parentheses.
 
+.. _sec-declaring-reactions:
+
 Declaring the Reactions
 ^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -223,7 +227,7 @@ The Transport Model
 ^^^^^^^^^^^^^^^^^^^
 
 A *transport model* is a set of equations used to compute transport
-properties. For one :class:`ideal_gas` phases, multiple transport models are
+properties. For :class:`ideal_gas` phases, multiple transport models are
 available; the one desired can be selected by assiging a string to this
 field. See :ref:`sec-gas-transport-models` for more details.
 
diff --git a/doc/sphinx/cti/species.rst b/doc/sphinx/cti/species.rst
index 576e4c793..5ff728034 100644
--- a/doc/sphinx/cti/species.rst
+++ b/doc/sphinx/cti/species.rst
@@ -90,6 +90,8 @@ at present, the properties needed are:
 
 See: :ref:`sec-thermo-models`
 
+.. _sec-species-transport-models:
+
 Species Transport Coefficients
 ------------------------------
 
diff --git a/interfaces/python/ctml_writer.py b/interfaces/python/ctml_writer.py
index 5e254a58b..ede36adb9 100644
--- a/interfaces/python/ctml_writer.py
+++ b/interfaces/python/ctml_writer.py
@@ -475,15 +475,16 @@ class species:
         :param thermo:
             The parameterization to use to compute the reference-state
             thermodynamic properties. This must be one of the entry types
-            described in ##REFF##. To specify multiple parameterizations, each
-            for a different temperature range, group them in parentheses.
+            described in :ref:`sec-thermo-models`. To specify multiple
+            parameterizations, each for a different temperature range,
+            group them in parentheses.
         :param transport:
             An entry specifying parameters to compute this species'
             contribution to the transport properties. This must be one of the
-            entry types described in ##REF##, and must be consistent with the
-            transport model of the phase into which the species is imported.
-            To specify parameters for multiple transport models, group the
-            entries in parentheses.
+            entry types described in :ref:`sec-species-transport-models`, and
+            must be consistent with the transport model of the phase into which
+            the species is imported. To specify parameters for multiple
+            transport models, group the entries in parentheses.
         :param size:
             The species "size". Currently used only for surface species,
             where it represents the number of sites occupied.
@@ -985,7 +986,7 @@ class reaction:
             four-digit numeric string beginning with 0001 for the first
             reaction in the file.
         :param options:
-            Processing options, as described in Section ##REF##
+            Processing options, as described in :ref:`sec-phase-options`.
         """
         self._id = id
         self._e = equation
@@ -1206,7 +1207,7 @@ class three_body_reaction(reaction):
             four-digit numeric string beginning with 0001 for the first
             reaction in the file.
         :param options:
-            Processing options, as described in ##REF##.
+            Processing options, as described in :ref:`sec-phase-options`.
         """
         reaction.__init__(self, equation, kf, id, '', options)
         self._type = 'threeBody'
@@ -1260,7 +1261,7 @@ class falloff_reaction(reaction):
             four-digit numeric string beginning with 0001 for the first
             reaction in the file.
         :param options:
-            Processing options, as described in ##REF##
+            Processing options, as described in :ref:`sec-phase-options`.
         """
         kf2 = (kf, kf0)
         reaction.__init__(self, equation, kf2, id, '', options)
@@ -1393,7 +1394,7 @@ class surface_reaction(reaction):
             four-digit numeric string beginning with 0001 for the first
             reaction in the file.
         :param options:
-            Processing options, as described in ##REF##
+            Processing options, as described in :ref:`sec-phase-options`.
         """
         reaction.__init__(self, equation, kf, id, order, options)
         self._type = 'surface'
@@ -1484,12 +1485,12 @@ class phase:
             The elements. A string of element symbols.
         :param species:
             The species. A string or sequence of strings in the format
-            described in ##REF##.
+            described in :ref:`sec-defining-species`.
         :param reactions:
             The homogeneous reactions. If omitted, no reactions will be
             included. A string or sequence of strings in the format described
-            in ##REF##. This field is not allowed for stoichiometric_solid
-            and stoichiometric_liquid entries.
+            in :ref:`sec-declaring-reactions`. This field is not allowed for
+            stoichiometric_solid and stoichiometric_liquid entries.
         :param kinetics:
             The kinetics model. Optional; if omitted, the default model for the
             phase type will be used.
@@ -2089,7 +2090,7 @@ class ideal_interface(phase):
         :param reactions:
             The heterogeneous reactions at this interface. If omitted, no
             reactions will be included. A string or sequence of strings in the
-            format described ##REF##.
+            format described in :ref:`sec-declaring-reactions`.
         :param site_density:
             The number of adsorption sites per unit area.
         :param phases: