diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py
index 4b35475b65..9b4afeb0f7 100644
--- a/cime_config/SystemTests/fsurdatmodifyctsm.py
+++ b/cime_config/SystemTests/fsurdatmodifyctsm.py
@@ -4,7 +4,7 @@
 
 import os
 import re
-from subprocess import check_call
+import subprocess
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
@@ -22,9 +22,6 @@ def __init__(self, case):
         if not os.path.exists(os.path.join(self._get_caseroot(),
             'done_FSURDATMODIFYCTSM_setup.txt')):
             # Create out-of-the-box lnd_in to obtain fsurdat_in
-            # TODO next two lines mess up the python environment.
-            # Need to find the right way to run ncar_pylib before
-            # tool_path below
             case.create_namelists(component='lnd')
             # If fsurdat_in does not exist, download it from the
             # server
@@ -69,19 +66,56 @@ def _create_config_file(self):
 
 
     def _run_modify_fsurdat(self):
-        """ 
-        Run the tool similarly to what you did for the python system test
-        """ 
-
-        # Hardcode for cheyenne until we come up with a robust
-        # way of ensuring the correct python environment is loaded
         tool_path = os.path.join(self._ctsm_root,
-            'tools/modify_fsurdat/fsurdat_modifier')
-        tool_command = tool_path + ' ' + self._cfg_file_path
-        check_call(tool_command, shell=True)
+                                 'tools/modify_fsurdat/fsurdat_modifier')
+
+        # Need to specify a specific python version that has the required dependencies
+        python_path = _get_python_path()
 
+        subprocess.check_call([python_path, tool_path, self._cfg_file_path])
 
     def _modify_user_nl(self):
         append_to_user_nl_files(caseroot = self._get_caseroot(),
                                 component = "clm",
                                 contents = "fsurdat = '{}'".format(self._fsurdat_out))
+
+def _get_python_path():
+    """Get path to ncar_pylib's python on cheyenne
+
+    This is needed because we need a python environment that includes xarray and its
+    dependencies. This is currently hard-coded for cheyenne until we come up with a robust
+    way in CIME of ensuring the correct python environment is loaded.
+
+    """
+    out = subprocess.check_output(['/glade/u/apps/opt/ncar_pylib/ncar_pylib', '-l'],
+                                  universal_newlines=True)
+
+    # First look for a loaded ('L') python
+    path = _find_path_from_pylib_output(out, 'L')
+    # If no loaded python found, look for a default ('D') python
+    if path is None:
+        path = _find_path_from_pylib_output(out, 'D')
+
+    if path is None:
+        raise RuntimeError('No python found')
+
+    return os.path.join(path, 'bin', 'python')
+
+def _find_path_from_pylib_output(ncar_pylib_output, char):
+    """Given line-by-line output from ncar_pylib, return the path to python if found
+
+    Args:
+    - ncar_pylib_output: line-by-line output from ncar_pylib
+    - char: the character to look for in the leading parenthetical expression (typically 'L' or 'D')
+
+    Returns a path to python, or None if not found
+    """
+    # The line of interest looks like the following (for char = 'L'):
+    # (L) ... /path/to/python
+    regex = r'\(' + char + r'\).* (/\S+)'
+    for line in ncar_pylib_output.splitlines():
+        match_line = re.match(regex, line)
+        if match_line:
+            return match_line.group(1)
+
+    return None