Ms Waters, from the left-wing Greens party, fed two-month-old daughter Alia Joy during a vote on Tuesday.
The lower house last year joined the Senate in allowing breastfeeding, but no MPs in either house had done so.
It followed a backlash in 2015 when Kelly O'Dwyer, a government minister, was asked to consider expressing milk to avoid missing parliamentary duties.
"We need more women and parents in Parliament," Ms Waters said on Facebook.