diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
index 53ceb4351c..1256fbbeba 100644
--- a/cmake/SetupBOUTThirdParty.cmake
+++ b/cmake/SetupBOUTThirdParty.cmake
@@ -186,6 +186,12 @@ if (BOUT_USE_NETCDF)
       set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${NETCDF_LDFLAGS_STRING}")
     endif()
   endif()
+  if (netCDF_DIR)
+    set(netCDF_ROOT "${netCDF_DIR}")
+  endif()
+  if (netCDFCxx_DIR)
+    set(netCDFCxx_ROOT "${netCDFCxx_DIR}")
+  endif()
 endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
@@ -299,6 +305,9 @@ if (BOUT_USE_SUNDIALS)
       message(FATAL_ERROR "SUNDIALS_VERSION 4.0.0 or newer is required. Found version ${SUNDIALS_VERSION}.")
     endif()
   endif()
+  if (SUNDIALS_DIR)
+    set(SUNDIALS_ROOT "${SUNDIALS_DIR}")
+  endif()
   target_link_libraries(bout++ PUBLIC SUNDIALS::nvecparallel)
   target_link_libraries(bout++ PUBLIC SUNDIALS::cvode)
   target_link_libraries(bout++ PUBLIC SUNDIALS::ida)