diff --git a/install/DEFAULTS.inc b/install/DEFAULTS.inc
index ec7793b67..dc59400c6 100644
--- a/install/DEFAULTS.inc
+++ b/install/DEFAULTS.inc
@@ -520,6 +520,18 @@ else
     endif
 endif
 
+# Embed the netcdf library directories in the executables.  Without this the
+# codes link against $(NETCDFDIR) but resolve at run time against whatever the
+# loader finds first, which fails with e.g.
+#   symbol lookup error: undefined symbol: netcdf_mp_nf90_create_
+# when a system netcdf shadows the bundled one, and silently mixes libraries
+# when the two were built by different compilers.
+NETCDF_RPATH = -Wl,-rpath,$(NETCDFDIR)
+ifneq ($(NETCDF_C_DIR),$(NETCDFDIR))
+    NETCDF_RPATH += -Wl,-rpath,$(NETCDF_C_DIR)
+endif
+NETCDF_EXTRA_LIBS += $(NETCDF_RPATH)
+
 # Intel specifics
 #----------------
 # include compiler specific libs for intel fast moves
diff --git a/install/TARGETS.inc b/install/TARGETS.inc
index b596e8c0a..0cbc65125 100644
--- a/install/TARGETS.inc
+++ b/install/TARGETS.inc
@@ -43,8 +43,9 @@ netcdf-c: v hdf5
 	cd ../; git submodule update --init deps/src/netcdf-c;
 	if [ ! -f ../deps/src/netcdf-c/Makefile ]; then \
 		cd ../deps/src/netcdf-c; \
+			CC="$(CC)" FC="$(FC)" F77="$(FC)" \
 			CPPFLAGS="-I$(realpath $(DEPSINSTALLDIR))/include" \
-			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib" \
+			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib -Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
 			./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
 	fi
 	cd ../deps/src/netcdf-c; \
@@ -56,8 +57,9 @@ netcdf-fortran: v netcdf-c
 	cd ../; git submodule update --init deps/src/netcdf-fortran;
 	if [ ! -f ../deps/src/netcdf-fortran/Makefile ]; then \
 		cd ../deps/src/netcdf-fortran; \
+			CC="$(CC)" FC="$(FC)" F77="$(FC)" \
 			CPPFLAGS="-I$(realpath $(DEPSINSTALLDIR))/include" \
-			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib" \
+			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib -Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
 			./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
 	fi
 	cd ../deps/src/netcdf-fortran; \
@@ -69,6 +71,8 @@ hdf5: v
 	cd ../; git submodule update --init deps/src/hdf5;
 	if [ ! -f ../deps/src/hdf5/Makefile ]; then \
 		cd ../deps/src/hdf5; \
+		CC="$(CC)" FC="$(FC)" \
+		LDFLAGS="-Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
 		./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
 	fi
 	cd ../deps/src/hdf5; \
diff --git a/install/makefile b/install/makefile
index 056de2ab6..f1912b8ef 100644
--- a/install/makefile
+++ b/install/makefile
@@ -116,6 +116,22 @@ realclean: clean clear
 # only for regenerating it when source USE/MODULE relationships change, and
 # require python3 (used by maintainers and the CI deps job, not end users).
 PYTHON ?= python3
+# Remove the autotools configuration of the bundled dependencies.  The netcdf
+# and hdf5 rules only run ./configure when no Makefile is present, so a plain
+# `clean` keeps whatever toolchain configured them first.  Switching FC/CC
+# without this leaves gfortran-built module files in place, and the codes then
+# fail with a confusing "module file was not generated by any release of this
+# compiler" followed by cascading kind-parameter errors.
+.PHONY: depsclean
+depsclean:
+	for d in hdf5 netcdf-c netcdf-fortran; do \
+		if [ -f ../deps/src/$$d/Makefile ]; then \
+			(cd ../deps/src/$$d && $(MAKE) distclean >/dev/null 2>&1 || true); \
+		fi; \
+		rm -f ../deps/src/$$d/Makefile ../deps/src/$$d/config.cache; \
+	done
+	rm -rf ../deps/lib/* ../deps/include/* ../deps/bin/* ../deps/share ../deps/hdf5
+
 .PHONY: deps checkdeps
 deps:
 	$(PYTHON) gen_deps.py > DEPENDENCIES.inc