Al-Wathiq was the son of al-Mu'tasim by a Byzantine Greek slave, Qaratis. He was named Harun after his grandfather, Caliph Harun al-Rashid (r. 786–809). Qaratis accompanied al-Wathiq's brother Jafar (the future caliph al-Mutawakkil) on the pilgrimage in 842, but she died on the way at al-Hirah, on August 16, 842. She was buried in Kufa.
When al-Mu'tasim died on 5 January 842, al-Wathiq succeeded him without opposition. His reign was brief and unremarkable, being essentially a continuation of al-Mu'tasim's own, as the government continued to be led by the men al-Mu'tasim had raised to power: the Turks Itakh, Wasif, and Ashinas, the vizier Muhammad ibn al-Zayyat, and the chief qādī, Ahmad ibn Abi Duwad.
In 843/4, the Caliph—allegedly at the instigation of the vizier Ibn al-Zayyat, or according to a story reported by al-Tabari, inspired by the downfall of the Barmakids under Harun al-Rashid—arrested, tortured, and imposed heavy fines on several of the secretaries in the central government, in an effort to raise money to pay the Turkish troops, and at the same time reduce the power of the leading Turkish commanders, such as Itakh and Ashinas, since most of the secretaries arrested and forced to pay were in their service.
In spring 845, a tribal rebellion broke out around Medina. A local tribe, the Banu Sulaym, had become embroiled in a conflict with the tribes of Banu Kinanah and Bahilah around Medina, resulting in clashes that left some dead (February/March 845). The local governor, Muhammad ibn Salih ibn al-Abbas, sent Hammad ibn Jarir al-Tabari against them with a mixed force, comprising regular troops as well as inhabitants of Medina, from the Ansar families and the Quraysh. Although the Banu Sulaym, not more than around 650 strong, were reluctant to fight, Hammad attacked them, only to be defeated and killed with almost his entire force. The Banu Sulaym now looted the environs of Mecca and Medina, and in May al-Wathiq charged one of his Turkish generals, Bugha al-Kabir (the Elder), to handle the affair. Accompanied by troops from the Shakiriyyah, Turkish, and the Magharibah guard regiments, Bugha defeated part of the Sulaym at the town of al-Suwariqiyyah, and forced most of the tribe to surrender. He imprisoned about a 1,000 of the tribe at Medina, and let the rest free. After going to Medina and Mecca in August, he also forced the Banu Hilal to submit on the same terms. After a few months, the prisoners, some 1,300 in total, tried to escape, but were thwarted by the Medinese, who proceeded to lay siege on the palace used as a prison. The prisoners were all killed in the ensuing clashes, and many tribesmen who happened to be in Medina suffered the same fate. In the meantime, Bugha used the opportunity to intimidate the Bedouin tribes of the region, and marched to confront the Banu Fazara and the Banu Murra. The tribes fled before his advance, with many submitting, and others fleeing to al-Balqa. Bugha then subdued the Banu Kilab, taking some 1,300 of them as prisoners back to Medina in May 846.
Like his father, al-Wathiq was an ardent Mu'tazilite, but also maintained good relations with the Alids. In 846, a well-respected notable, Ahmad ibn Nasr ibn Malik al-Khuza'i, a descendant of one of the original missionaries of the Abbasid Revolution, launched a plot in Baghdad to overthrow al-Wathiq, his Turkish commanders, and the Mu'tazilite doctrines. The uprising was scheduled for the night of 4 April 846. However, those who were supposed to sound a drum as the signal to rise did so a day early, and there was no response. The Mus'abid deputy governor of the city, Muhammad ibn Ibrahim—the governor, his brother Ishaq, was absent—inquired on the event, and the conspiracy was revealed. Ahmad ibn Nasr and his followers were arrested and brought before al-Wathiq. The caliph interrogated him publicly, though more on the thorny issue of the createdness of the Quran rather than on the rebellion. Ahmad's answers enraged al-Wathiq so much, that the Caliph took al-Samsamah, a famous sword of the pre-Islamic period, and personally joined in the execution of Ahmad, along with the Turks Bugha al-Sharabi and Sima al-Dimashqi. Ahmad's corpse was publicly displayed at the gibbet of Babak in Baghad, while twenty of his followers were thrown into prison.
The same year there was a break in at the public treasury (bayt al-mal) in Samarra. Thieves made off with 42,000 silver dirhams and a small amount of gold dinars. The ṣāḥib al-shurṭa, Yazid al-Huwani, a deputy of Itakh, pursued and caught them.
In A.H. 232 (846–847) al-Wathiq sent Bugha al-Kabir to stop the depredations of the Banu Numayr. In al-Yamamah on February 4, 847 he fought a major engagement against them. At first he was hard pressed. Then some troops he had out raiding returned, fell upon the forces attacking Bugha and completely routed them.
In 838 al-Mu'tasim had scored a major victory against the Abbasid Caliphate's perennial foe, the Byzantine Empire, with the celebrated Sack of Amorium. He did not follow up this success, however, and warfare reverted to the usual raids and counter-raids along the border. At the time of his death in 842, al-Mu'tasim was preparing yet another large-scale invasion, but the great fleet he had prepared to assault Constantinople perished in a storm off Cape Chelidonia a few months later. Following al-Mu'tasim's death, the Byzantine regent Theoktistos attempted to reconquer the Emirate of Crete, an Abbasid vassal, but the campaign ended in disaster. In 844, an army from the border emirates of Qaliqala and Tarsus, led by Abu Sa'id, and possibly the emir of Malatya Umar al-Aqta, raided deep into Byzantine Asia Minor and reached as far as the shore of the Bosporus. The Muslims then defeated Theoktistos at the Battle of Mauropotamos, aided by the defection of senior Byzantine officers.
In 845, a Byzantine embassy arrived at the caliphal court, to negotiate about a prisoner exchange. It was held in September of the same year under the auspices of Khaqan al-Khadim, and 4,362 Muslims were set free. A winter raid by the Abbasid governor of Tarsus shortly after failed disastrously, after which the Arab-Byzantine frontier remained quiet for six years.
Al-Wathiq died as the result of being treated for dropsy by being seated in an oven, on 10 August 847. His age is variously given as 32, 34, or 36 years at the time. He was succeeded by his half-brother, al-Mutawakkil.
Al-Tabari records that al-Wathiq was of medium height, handsome and well-built. He was fair with a ruddy complexion. His left eye was paralyzed.
Al-Wathiq is one of the more obscure Abbasid caliphs. According to the historian Hugh Kennedy, "no other caliph of the period has left so little trace of the history of his times, and it is impossible to form any clear impression of his personality", while the Encyclopaedia of Islam writes that "he had not the gifts of a great ruler, and his brief reign was not distinguished by remarkable events". He is reported as having been generous to the poor of the holy cities of Mecca and Medina, but he did not enjoy any great popularity. What is known of his character shows him being given to indolence and the pleasures of court life: himself active as a composer, al-Wathiq was a patron of poets, singers and musicians. He is known for the favour he showed to the singer Mukhariq, and confirmed al-Dahhak al-Bahili, known as al-Khalīʿ, "the debauched one", as court poet. The sources also relate some episodes that show al-Wathiq's "intellectual curiosity": he reportedly dreamed that the "Barrier of Dhu'l-Qarnayn" had been breached—probably resulting from news of the movements of the Kirghiz Turks at the time that caused large population shifts among the Turkic nomads of Central Asia—and sent Sallam al-Tarjman to journey to the region and investigate. Likewise, according to Ibn Khordadbeh the Caliph sent the astronomer al-Khwarizmi to the Byzantines to investigate the legend of the Seven Sleepers of Ephesus.
His very obscurity allowed William Beckford to present a heavily fictionalized version of al-Wathiq in his classic 18th-century Gothic fantasy novel Vathek, "a fantastic tale of cruelty, dissipation and a search for the lost treasure of ancient kings, guarded by Iblis/Satan himself".