Waterston, 35, who is British, will play the role of Tina, or Porpentina, a witch who operates in the US, said the Hollywood Reporter.
The setting is a switch from the Potter books, which were set in London and other parts of England.
According to Warner Bros, Porpentina meets magizoologist Newt Scamander (Redmayne) when he stops in New York City on his travels to find and document magical creatures.
David Yates, who directed of the last four "Harry Potter" films, will helm the project which has a screenplay by Potter author J K Rowling.
Waterston appeared in Boardwalk Empire and had a star turn in "Vice", which was directed by Paul Thomas Anderson.
She will portray Chrisann Brennan, Steve Jobs' girlfriend, in the upcoming Jobs biopic directed by Danny Boyle.
