Aborigines at the time suffered significant discrimination and disadvantages in Australian society, such as restrictions on movement, residence, employment, and access to services and citizenship. Born in northern New South Wales and raised in Queensland, Waters was working as a shearer when he joined the RAAF in 1942. Training initially as a mechanic, he volunteered for flying duties and graduated as a sergeant pilot in 1944. He flew P-40 Kittyhawks in the South West Pacific theatre, where he completed 95 missions, mainly close air support. By the end of the war he had risen to the rank of warrant officer. Following his discharge from the RAAF in 1946, he attempted to start a regional airline but was unable to secure financial backing and government approval. He went back to shearing, and died in 1993 at the age of 69.
Waters undertook his basic flight instruction at No. 1 Elementary Flying Training School in Narrandera, New South Wales, where he flew De Havilland Tiger Moths. He completed his training on CAC Wirraways and received his wings as a sergeant pilot at No. 5 Service Flying Training School in Uranquinty. Posted to No. 2 Operational Training Unit at Mildura, Victoria, he converted to P-40 Kittyhawk fighters. Once, while he was on leave, Waters was reportedly gaoled in Moree, New South Wales, for not carrying an identity card, which was one of the racially discriminatory institutions affecting Aborigines at the time. On 14 November 1944, he was posted to No. 78 Squadron, a fighter unit based on the island of Noemfoor, off Dutch New Guinea. When he arrived, he was allocated a P-40 Kittyhawk. By chance, a previous pilot had nicknamed the plane "Black Magic" and painted those words on its nose. Waters found the name of his plane an amusing coincidence and chose to retain it.
One of Len Waters' brothers, Donald Edward (Jimmy) Waters, had served as an infantryman with the Australian Army during the war. With the end of the Pacific War in September 1945, Len considered volunteering for the Australian component of the British Commonwealth Occupation Force in Japan, if his brother did also. Jim declined at the time (he later changed his mind), so Len returned to Australia and left the air force with the rank of warrant officer on 18 January 1946.
Four weeks after his discharge from the Air Force, Waters married Gladys Saunders, with whom he had six children. He worked as an automotive mechanic, but was forced to cease by union rules, which required him to serve an apprenticeship. Waters was then briefly employed by a local council in Queensland as a road worker, before returning to shearing, which took him away from his family to properties stretching from North Queensland to Victoria. He personally estimated that he sheared a million sheep during his life.
Waters applied for housing commission accommodation and was allocated a house at Inala, Brisbane, in August 1956. He eventually bought the property and lived there for 33 years. He died on 24 August 1993 at the age of 69 in Cunnamulla, and was buried in St George Cemetery.
In 1995–96, Waters was commemorated in several ways: Australia Post depicted his portrait on a stamp and that of his P-40 Kittyhawk fighter "Black Magic" on an aérogramme, as part of its Australia Remembers series; Black Magic Port was named after his personal Kittyhawk; Len Waters Place, a park in Inala, was opened; Moree Plains Shire Council dedicated Leonard Waters Park in Boggabilla, New South Wales; and Len Waters Street in Ngunnawal, Australian Capital Territory, was named after him. In 2003, Balonne Shire Council erected a monument to Waters and another local RAAF identity, Squadron Leader John Jackson, in St George. In 2011, the Sutherland Shire Council recognised Len Waters' memory and achievements by dedicating Len Waters Park, with a memorial plinth and plaque, at Timbrey Circuit, Barden Ridge, New South Wales.