Check that you have the correct NetCDF libraries installed. NetCDF C & Fortran Libraries - NetCDF C Version 4.4.1.1 and NetCDF F Version 4.4.4 or greater available from https://www.unidata.ucar.edu/software/netcdf/ (These libraries need to be compiled with the same compilers as you will use to compile WRF-Hydro) Note: if you are coupling with WRF, the WRF user guide instructs users to build netCDF 4 with the --disable-netcdf-4 flag. However netCDF 4 must be enabled to work with WRF-Hydro. Please check that this flag has been enabled.
See if there were any diagnostic files created. If not, recompile and re-run with HYDRO_D=1 to see if you receive additional diagnostic output that may help determine what the issue is.