diff --git a/CHANGES b/CHANGES
index 4379871aa..03d3425ed 100644
--- a/CHANGES
+++ b/CHANGES
@@ -79,6 +79,9 @@ Bugs fixed
 * #1017: Be helpful and tell the user when the argument to :rst:dir:`option`
   does not match the required format.
 
+* #1345: Fix two bugs with :confval:`nitpick_ignore`; now you don't have to
+  remove the store environment for changes to have effect.
+
 Documentation
 -------------
 
diff --git a/doc/config.rst b/doc/config.rst
index ac6d506b2..5776dbb69 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -236,7 +236,8 @@ General configuration
 
    A list of ``(type, target)`` tuples (by default empty) that should be ignored
    when generating warnings in "nitpicky mode".  Note that ``type`` should
-   include the domain name.  An example entry would be ``('py:func', 'int')``.
+   include the domain name if present.  Example entries would be ``('py:func',
+   'int')`` or ``('envvar', 'LD_LIBRARY_PATH')``.
 
    .. versionadded:: 1.1
 
diff --git a/doc/invocation.rst b/doc/invocation.rst
index c6125ecc5..107a50aa2 100644
--- a/doc/invocation.rst
+++ b/doc/invocation.rst
@@ -140,7 +140,8 @@ The :program:`sphinx-build` script has several options:
 .. option:: -n
 
    Run in nit-picky mode.  Currently, this generates warnings for all missing
-   references.
+   references.  See the config value :confval:`nitpick_ignore` for a way to
+   exclude some references as "known missing".
 
 .. option:: -N
 
diff --git a/sphinx/config.py b/sphinx/config.py
index 4cca4b357..8b15bdf3b 100644
--- a/sphinx/config.py
+++ b/sphinx/config.py
@@ -72,7 +72,7 @@ class Config(object):
         primary_domain = ('py', 'env'),
         needs_sphinx = (None, None),
         nitpicky = (False, 'env'),
-        nitpick_ignore = ([], 'env'),
+        nitpick_ignore = ([], 'html'),
 
         # HTML options
         html_theme = ('default', 'html'),
diff --git a/sphinx/environment.py b/sphinx/environment.py
index 919ae7102..a319ef3c1 100644
--- a/sphinx/environment.py
+++ b/sphinx/environment.py
@@ -177,9 +177,6 @@ class BuildEnvironment:
         # this is to invalidate old pickles
         self.version = ENV_VERSION
 
-        # make this a set for faster testing
-        self._nitpick_ignore = set(self.config.nitpick_ignore)
-
         # All "docnames" here are /-separated and relative and exclude
         # the source suffix.
 
@@ -440,6 +437,9 @@ class BuildEnvironment:
         self.find_files(config)
         self.config = config
 
+        # this cache also needs to be updated every time
+        self._nitpick_ignore = set(self.config.nitpick_ignore)
+
         added, changed, removed = self.get_outdated_files(config_changed)
 
         # allow user intervention as well
@@ -1385,6 +1385,9 @@ class BuildEnvironment:
                 dtype = domain and '%s:%s' % (domain.name, typ) or typ
                 if (dtype, target) in self._nitpick_ignore:
                     warn = False
+                # for "std" types also try without domain name
+                if domain.name == 'std' and (typ, target) in self._nitpick_ignore:
+                    warn = False
         if not warn:
             return
         if domain and typ in domain.dangling_warnings: