Sitting director Andy Macfarlane has also been re-elected for another three-year term.
There were three candidates vying for two board seats: Mike Fleming, chair of Fortuna Group missed out.
Watters replaces Edgecumbe farmer Donna Smit who retires from the board after serving for six years.
Watters, her husband Andrew and other family, own a 510-cow dairy unit in the Wairarapa.
Currently she is the chair of AsureQuality, a director of LIC, and a director of MetService.
Watters takes up her directorship at Fonterra’s annual general meeting in Rotorua on Thursday.