From 1997, Waters was an honorary senior research fellow at Massey University's Albany campus, where his wife Joyce was a professor of chemistry.
In 2002, Massey Universitys governing council considered restoring Waters to the vice-chancellorship as an interim replacement following the retirement of his successor, James McWha; however, the board was prevented from doing so by the State Sector Act 1988, which barred the appointment of someone not already on the universitys payroll; Waters had since moved to Auckland and no longer worked in the university sector.
Waters died in Auckland on 7 June 2018, aged 87.