Biwott had a daughter in an early relationship. Later, during his time studying in Australia, Biwott met Dutch-born Hannie, whom he married in 1963 and with whom he had two daughters. Subsequently, in new relationships, he had a daughter with Margaret Kamar and two daughters and a son with Callista Mathews.
Suffering from the effects of end-stage kidney disease, Nicholas Biwott spent his last months surrounded by his family and friends. He died aged 77, on 11th July 2017, at The Nairobi Hospital.
His funeral service was held at AIC Milimani Church in Nairobi on 18th July 2017, presided over by the Rev. Dr. Matthews Mwalw’a. Such was the demand for a hero’s send-off to be given to Biwott, community leaders and clergy of different denominations and faiths organised an event to honour him in his constituency, followed by a larger memorial service at the girls’ school Biwott built in memory his mother, the Maria Soti Educational Centre. In all, more than 20,000 people attended these three commemorations of Biwott’s life, including President Kenyatta; the Leader of the Opposition, Raila Odinga; the Kenyan Cabinet, past and present; dignitaries from East Africa, such as the former President of Tanzania, Jakaya Kikwete; Heads of the Civil Service, industry and charities, as well as friends and thousands of constituents, young and old.