Hello, The system voltage would be to what system you would use the unit. You can use it in 12, 24, or 48 volts system. I know you will use 12 volts batteries but depending on how you would connect them, then that would be your system voltage. If you would use your 12 volts deep cycle battery, as a 12 volts system, then use 12 volts as your system voltage. Even though the output of the solar panel is 30 volts, that is the function of the controller, to harvest those big voltages and use them to charge the 12 volts battery , which would be your system voltage as well. use 12 volts as you system voltage if you will connect the batteries in parallel as a 12 volts battery bank.