diff --git a/src/pflotran/makefile b/src/pflotran/makefile
index 17587c91d..7caf73e8c 100644
--- a/src/pflotran/makefile
+++ b/src/pflotran/makefile
@@ -51,7 +51,7 @@ PETSC_MAKE_STOP_ON_ERROR=
 # so that PFLOTRAN will be built with the same options as 
 # the petsc configured in $PETSC_DIR/$PETSC_ARCH
 
-MYFLAGS = -I. 
+MYFLAGS = -I. -L@HDF5_FORTRAN_LIBS@ -I@HDF5_FORTRAN_INCLUDE@
 
 ###############################################################################
 # Preprocessor flags for special PFLOTRAN features/hacks
@@ -183,7 +183,7 @@ ifdef ug_mpi_scatter_ghost
 endif
 
 ifdef have_hdf5
-LIBS +=  -L${HDF5_LIB} -lhdf5_fortran -lhdf5 -lz 
+LIBS +=  -L${HDF5_LIB} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub -lz
 endif
 
 # Set this accordingly on your platform
@@ -273,7 +273,7 @@ pflotran_rxn_obj = ${pflotran_src}pflotran_rxn.o
 
 # PFLOTRAN executable
 pflotran : $(pflotran_obj)
-	${FLINKER} -o pflotran $(pflotran_obj) ${PETSC_LIB} ${LIBS} 
+	${FLINKER} -o pflotran $(pflotran_obj) ${PETSC_LIB} ${LIBS} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub
 
 # PFLOTRAN as a library
 libpflotran.a : $(pflotran_obj)
@@ -286,11 +286,11 @@ libpflotranchem.a : $(chem_obj) $(shared_mode_aux_obj) $(util_obj)
 # object files lists below.... This is a workaround.
 pflotran_rxn : libpflotranchem.a $(pflotran_rxn_obj)
 	${FLINKER} -o $@ $(pflotran_rxn_obj) $(chem_obj) $(shared_mode_aux_obj) \
-	$(util_obj) ${PETSC_LIB} ${LIBS} 
+	$(util_obj) ${PETSC_LIB} ${LIBS} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub
 
 # PFLOTRAN derivative test
 pflotran_derivative : $(pflotran_base_obj) pflotran_derivative.o
-	${FLINKER} -o pflotran_derivative $(pflotran_base_obj) pflotran_derivative.o ${PETSC_LIB} ${LIBS} 
+	${FLINKER} -o pflotran_derivative $(pflotran_base_obj) pflotran_derivative.o ${PETSC_LIB} ${LIBS} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub
 
 $(SRC_DIR)/pflotran_provenance.F90 : FORCE
 ifeq ($(UPDATE_PROVENANCE),1)