diff --git a/install/DEFAULTS.inc b/install/DEFAULTS.inc
index e0ff8be1d..dfb9024bd 100644
--- a/install/DEFAULTS.inc
+++ b/install/DEFAULTS.inc
@@ -440,6 +440,10 @@ else
     $(error "Unsupported C compiler. Must set environment variable CC to a C compiler (e.g. gcc, icc, pgcc)")
 endif
 
+# Pass the selected toolchain to dependency configure scripts and sub-makes.
+export FC CC
+export F77 = $(FC)
+
 # List of needed dependencies, will be appended if math or netcdf
 # libraries are not found
 NEEDED_DEPS = 
@@ -560,6 +564,14 @@ else
     endif
 endif
 
+# Embed the configured netcdf library directories for runtime lookup.
+# These paths must remain available when running the executables.
+NETCDF_RPATH = -Wl,-rpath,$(NETCDFDIR)
+ifneq ($(NETCDF_C_DIR),$(NETCDFDIR))
+    NETCDF_RPATH += -Wl,-rpath,$(NETCDF_C_DIR)
+endif
+NETCDF_EXTRA_LIBS += $(NETCDF_RPATH)
+
 # Intel specifics
 #----------------
 # include compiler specific libs for intel fast moves
diff --git a/install/TARGETS.inc b/install/TARGETS.inc
index b596e8c0a..e20d93276 100644
--- a/install/TARGETS.inc
+++ b/install/TARGETS.inc
@@ -44,7 +44,7 @@ netcdf-c: v hdf5
 	if [ ! -f ../deps/src/netcdf-c/Makefile ]; then \
 		cd ../deps/src/netcdf-c; \
 			CPPFLAGS="-I$(realpath $(DEPSINSTALLDIR))/include" \
-			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib" \
+			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib -Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
 			./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
 	fi
 	cd ../deps/src/netcdf-c; \
@@ -57,7 +57,7 @@ netcdf-fortran: v netcdf-c
 	if [ ! -f ../deps/src/netcdf-fortran/Makefile ]; then \
 		cd ../deps/src/netcdf-fortran; \
 			CPPFLAGS="-I$(realpath $(DEPSINSTALLDIR))/include" \
-			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib" \
+			LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib -Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
 			./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
 	fi
 	cd ../deps/src/netcdf-fortran; \
@@ -69,6 +69,7 @@ hdf5: v
 	cd ../; git submodule update --init deps/src/hdf5;
 	if [ ! -f ../deps/src/hdf5/Makefile ]; then \
 		cd ../deps/src/hdf5; \
+		LDFLAGS="-Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
 		./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
 	fi
 	cd ../deps/src/hdf5; \
diff --git a/install/makefile b/install/makefile
index 056de2ab6..46e02b303 100644
--- a/install/makefile
+++ b/install/makefile
@@ -103,19 +103,23 @@ clear:
 	cd ../docs/examples/solovev_kinetic_example; rm -f *.out *.bin *.nc
 	cd ../docs/examples/solovev_resistive_example; rm -f *.out *.bin *.nc *.dat
 
-# Revert to clean state
+# Remove build products and dependency configuration before switching compilers.
+# Dependency sources stay in ../deps/src; custom install prefixes are respected.
 realclean: clean clear
 	rm -rf ../deps/lib/* ../deps/hdf5 ../deps/include/* ../deps/bin/* ../deps/share ../bin
 	if [ -f ../deps/src/OpenBLAS/Makefile ]; then cd ../deps/src/OpenBLAS && make clean; fi
-	if [ -f ../deps/src/hdf5/Makefile ]; then cd ../deps/src/hdf5 && make clean; fi
-	if [ -f ../deps/src/netcdf-c/Makefile ]; then cd ../deps/src/netcdf-c && make clean; fi
-	if [ -f ../deps/src/netcdf-fortran/Makefile ]; then cd ../deps/src/netcdf-fortran && make clean; fi
+	if [ -f ../deps/src/hdf5/Makefile ]; then cd ../deps/src/hdf5 && $(MAKE) distclean; fi
+	if [ -f ../deps/src/netcdf-c/Makefile ]; then cd ../deps/src/netcdf-c && $(MAKE) distclean; fi
+	if [ -f ../deps/src/netcdf-fortran/Makefile ]; then cd ../deps/src/netcdf-fortran && $(MAKE) distclean; fi
+	rm -f "$(DEPSINSTALLDIR)"/lib/libnetcdf* "$(DEPSINSTALLDIR)"/lib/libhdf5* \
+		"$(DEPSINSTALLDIR)"/include/netcdf*.mod "$(DEPSINSTALLDIR)"/include/typesizes.mod
 
 # Dependency graph (DEPENDENCIES.inc) maintenance.
 # Building GPEC never needs these -- DEPENDENCIES.inc is committed. They are
 # 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
+
 .PHONY: deps checkdeps
 deps:
 	$(PYTHON) gen_deps.py > DEPENDENCIES.inc