diff --git a/darshan-runtime/darshan-config.in b/darshan-runtime/darshan-config.in
index 5ae43c09f6e39bc17928f4f672df6e9219c1015a..5863eaa1aab67e72c10515b49e4bd69fbf1caa13 100755
--- a/darshan-runtime/darshan-config.in
+++ b/darshan-runtime/darshan-config.in
@@ -4,8 +4,15 @@ CP_WRAPPERS="@CP_WRAPPERS@"
 DARSHAN_LIB_PATH="@darshan_lib_path@"
 DARSHAN_LD_FLAGS="@LDFLAGS@"
 
+# NOTE:
+# - we deliberately list libdarshan-mpi-io twice in the link command.  The
+#   first is necessary to correctly use the MPI profiling interface.  The
+#   final one is necessary to give the linker a change to resolve indirect
+#   dependencies on PnetCDF and HDF5 symbols (if the app used a library which 
+#   in turn used one of those HLLs).
 PRE_LD_FLAGS="-L$DARSHAN_LIB_PATH $DARSHAN_LD_FLAGS -ldarshan-mpi-io -lz $CP_WRAPPERS"
-POST_LD_FLAGS="-L$DARSHAN_LIB_PATH -ldarshan-posix"
+POST_LD_FLAGS="-L$DARSHAN_LIB_PATH -ldarshan-posix -ldarshan-mpi-io"
+
 
 usage="\
 Usage: darshan-config [--pre-ld-flags] [--post-ld-flags]"