Waitoa is said to have been of Ngāti Raukawa, Ngāti Maru and Te Arawa descent. The names of his parents are not known. He is thought to have been born at Waitoa, near present day Morrinsville, and to have gone south to Horowhenua with one of the migrations of Ngāti Raukawa in the 1820s. He was an early convert of the CMS missionary Octavius Hadfield, and received his initial religious instruction in Christianity at Hadfield's mission at Waikanae. He took the name Rota (Lot), probably at his baptism by Hadfield on 17 October 1841. He attracted the attention of Bishop G. A. Selwyn on the latter's visit to Kapiti Island in November 1842. Waitoa volunteered to accompany Selwyn to Auckland, and for the next 12 years was the bishop's friend and travelling companion.
Waitoa was selected by Selwyn for training for the ministry. From 1843 he attended St John's College, which was established by Selwyn at Waimate North that year and in 1844 was shifted to Auckland. At St John's he was referred to as college butler and was in charge of provisions; he went on to study and became master of the junior department of the Māori boys' school, Abraham scholar and catechist. He was described as 'a man of integrity and exceptional intelligence', possessing a warm, generous nature. On 10 August 1848, at St John's Chapel, he married Te Rina Hinehuka of Ngāti Porou, a pupil at Margaret Kissling's school for Māori girls at Kohimarama. They had three children: Caroline Harriet, Wiremu Hēnare, and Hōne, who like his father was to become an Anglican clergyman.
Waitoa's ordination as deacon, the first ordination of a Māori into the Anglican church, at St Paul's, Auckland, on 22 May 1853, resolved many tensions that had built up between the CMS, Selwyn and the Māori people. Dissatisfaction had developed within the CMS over the theological instruction at St John's, and there was suspicion in some quarters that Selwyn was deliberately postponing the ordination of Māori. In early 1853, when an internal crisis caused the college to disperse temporarily, the Māori department had been closed. Waitoa's ordination also greatly increased his mana among his own churchpeople.
After his ordination Waitoa was appointed minister to the CMS station at Te Kawakawa (Te Araroa), East Coast. His appointment came at a critical time for the church. Many East Coast Māori, it seemed, were beginning to lose their faith in Christianity and their attachment to the mission appeared to be diminishing; increasing contact with European traders and settlements was seen by the missionaries as a dangerous influence. The Māori teachers proved inadequate to halt this apparent move away from the church, and the CMS would not provide further missionaries. Waitoa's appointment was the first to meet an urgent need for highly trained Māori clergy to provide supervision and spiritual guidance.
At the same time it brought potential conflict to the Māori community. Waitoa initially met much opposition from Te Houkāmau of Ngāti Porou, who had twice been denied baptism by William Williams and who resented a member of a tribe he did not esteem assuming the position of teacher and leader among his people. Later, however, Te Houkāmau was baptised by Waitoa. With Te Houkāmau, Rota Waitoa built St Stephen's Church at Te Araroa, and possibly St Barnabas's at Hicks Bay. The introduction of Māori clergy was only gradually accepted by the Māori however.
The size of the mission and the complexity of the theological and practical problems he encountered led Waitoa to return periodically to St John's, to read and study, and to renew his friendship with Selwyn. At the same time he was preparing for ordination to the priesthood. After the creation of the Waiapu diocese in 1858, to meet the need for its regular administration, he was ordained priest at Gisborne, by Bishop William Williams, on 4 March 1860; he was the first Māori priest. He retained his position as superintendent of Te Kawakawa pastorate. After Te Rina Hinehuka's death, probably in 1857, Waitoa married Hārata Tiarete of Te Kawakawa. There were two children of this second marriage: Perepetua, sometimes known as Penepetua, and Wiremu Iharaira.
Waitoa's last years were marked by increasing difficulties. The resistance of East Coast Māori to government land sale policies, resentment of government authority, and some popular support among Ngāti Porou for the King movement and Pai Mārire, came to a head with the outbreak of war on the East Coast in 1865. Waitoa was one of an important group of East Coast leaders who opposed the King movement and Pai Mārire, and in 1865–66 was involved in the hostilities. He continued his work throughout this period although at one time he was forced to abandon Te Kawakawa mission.
In 1866 a riding accident left Waitoa seriously injured. Selwyn invited him and his family back to Auckland. Waitoa died there on 22 July 1866, and was buried at St Stephen's cemetery, Judges Bay.