diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index df56c2af0944ee603f1467ec61431fa735ed3a47..5d9f20b6efb2e91c3367826070c96d1e7711f4d2 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -316,9 +316,9 @@ def CalculateSurfaceArea(entity,  radius=1.4,
       command = "%s %s -p %f " % \
                 (naccess_executable, naccess_data_file, radius)
       if include_hydrogens:
-        command = "%s -w" % command
-      if include_water:
         command = "%s -y" % command
+      if include_water:
+        command = "%s -w" % command
       if include_hetatm:
         command = "%s -h" % command
       # execute naccess