Already during the last months of al-Mu'tasim's life, a large-scale revolt had erupted in Palestine under a certain al-Mubarqa. Al-Mu'tasim sent the general Raja ibn Ayyub al-Hidari to confront the rebels. When al-Wathiq came to power, he dispatched al-Hidari against Ibn Bayhas, who led a Qaysi tribal revolt around Damascus. The exact relationship of this uprising with the revolt of al-Mubarqa is unclear. Taking advantage of the dissensions among the tribesmen, al-Hidari quickly defeated Ibn Bayhas, and then turned south and confronted al-Mubarqa's forces near Ramla. The battle was a decisive victory for the government army, with al-Mubarqa taken prisoner and brought to Samarra, where he was thrown into prison and never heard of again.
Upon coming to the throne, al-Wathiq appointed Khalid ibn Yazid al-Shaybani as governor of the restive province of Armenia. At the head of a large army, Khalid defeated the opposition of the local Muslim and Christian princes at the Battle of Kawakert. Khalid died soon after, but his son, Muhammad al-Shaybani, succeeded him in office and continued his father's task.
In spring 845, another tribal rebellion broke out. A local tribe, the Banu Sulaym, had become embroiled in a conflict with the tribes of Banu Kinanah and Bahilah around Medina, resulting in bloody clashes in February/March 845. The local governor, Salih ibn Ali, sent an army against them comprising regular troops as well as citizens of Medina, but the Sulaym were victorious and proceeded to loot the environs of the two holy cities. As a result, in May, al-Wathiq charged one of his Turkic generals, Bugha al-Kabir, to handle the affair. Accompanied by professional troops from the Shakiriyyahi, Turkic, and Magharibah guard regiments, Bugha defeated the Sulaym and forced them to surrender. In early autumn, he also forced the Banu Hilal to submit. Bugha's troops took many prisoners, some 1,300 in total who were held in Medina. They tried to escape, but were thwarted by the Medinese, and most were killed in the process. In the meantime, Bugha used the opportunity to intimidate the other 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.
A minor Kharijite uprising in 845/6 occurred in Diyar Rabi'a under a certain Muhammad ibn Abdallah al-Tha'labi (or Muhammad ibn Amr) but was easily suppressed by the governor of Mosul. In the same year, the general Wasif suppressed restive Kurdish tribes in Isfahan, Jibal and Fars.
In September 846, al-Wathiq sent Bugha al-Kabir to stop the depredations of the Banu Numayr in Yamamah. On February 4, 847, Bugha fought a major engagement against about 3,000 Numayris at the watering place of Batn al-Sirr. At first, he was hard pressed, and his forces almost disintegrated. Then some troops he had out raiding the Numayris' horses returned, fell upon the forces attacking Bugha and completely routed them. According to one report, up to 1,500 Numayris were killed. Bugha spent a few months pacifying the region, issuing writs of safe passage to those who submitted and pursuing the rest, before he returned to Basra in June/July 847. Over 2,200 Bedouin from various tribes were brought captive with him.
Like his father, al-Wathiq was an ardent Mu'tazilite — the sources agree that he was strongly influenced by the chief qadi, Ibn Abi Duwad — but also, like his father, maintained good relations with the Alids. In the third year of his caliphate, al-Wathiq revived the inquisition (mihna), sending officials to question jurists on their views on the controversial topic of the createdness of the Quran. Al-Wathiq supported the Mu'tazili view that the Quran was created and not eternal, and hence fell within the authority of a God-guided imam (i.e., the caliph) to interpret according to the changing circumstances. Even during a prisoner exchange held with the Byzantine Empire in 845, the ransomed Muslim prisoners were questioned on their opinions regarding the topic, with those giving unsatisfactory answers reportedly left to remain in captivity. Thus, Ahmad ibn Hanbal, the founder of the Hanbali school of jurisprudence, who opposed the Mu'tazili doctrine, was forced to cease his teachings and only resumed them after al-Wathiq's death.
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 Turkic commanders, and the Mu'tazilite doctrines. His followers distributed money to the people, and the date for the uprising was scheduled for the night of April 4/5, 846. However, according to al-Tabari, those who were supposed to sound a drum as the signal to rise got drunk and did so a day early, and there was no response. Khatib al-Baghdadi on the other hand reports simply that an informer gave the plot away to the authorities. The deputy governor of the city, Muhammad ibn Ibrahim — the governor, his brother Ishaq, was absent — inquired on the event, and the conspiracy was revealed. Al-Khuza'i and his followers were arrested and brought before al-Wathiq at Samarra.
The Caliph interrogated al-Khuza'i publicly, though more on the thorny theological issue of the createdness of the Quran rather than on the actual 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 next to the gibbet of Babak in Baghdad, 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 sahib al-shurta (chief of security), Yazid al-Huwani, a deputy of Itakh, pursued and caught them. Turner points out that this episode may provide some premonition of the crisis to erupt in later decades: security even at the main palace was lax, and, based on the thieves' loot, the treasury appears to have been almost empty at the time.
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 Amorion. This success was not followed up, and warfare reverted to the usual raids and counter raids along the border. According to Byzantine sources, 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. This event is not reported in Muslim sources.
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. At around the same time, the Paulicians, a sect persecuted as heretical in Byzantium, defected to the Arabs under their leader Karbeas. They founded a small principality on the Abbasid–Byzantine frontier, centered on the fortress of Tephrike, and henceforth joined the Arabs in their attacks on Byzantine territory.
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 Yazaman al-Khadim, and somewhere between 3,500–4,600 Muslims were ransomed. In March of the same year, however, 42 officers taken captive at Amorion were executed at Samarra, after refusing to convert to Islam. After the truce arranged for the exchange expired, the Abbasid governor of Tarsus, Ahmad ibn Sa'id ibn Salm, led a winter raid with 7,000 men. It failed disastrously, with 500 men dying of cold or drowning, and 200 taken prisoner. After this, the Arab-Byzantine frontier remained quiet for six years. Only in the west did the Abbasids' Aghlabid clients continue their gradual conquest of Byzantine Sicily, capturing Messina (842/43), Modica (845), and Leonntini (846). In 845/46, the Aghlabids captured Miseno near Naples in mainland Italy, and in the next year their ships appeared in the Tiber River and their crews raided the environs of Rome.
Al-Wathiq died as the result of edema, likely from liver damage or diabetes, while being seated in an oven in an attempt to cure it, on August 10, 847. His age is variously given as 32, 34, or 36 in Islamic years at the time of his death. He was buried in the Haruni Palace in Samarra.
Al-Wathiq death was unexpected and left the succession open — although the near-contemporary historian al-Ya'qubi claims that an heir had been named, and the oath of allegiance given to him. Consequently, the leading officials, the vizier, Ibn al-Zayyat, the chief qadi, Ahmad ibn Abi Duwad, the Turkic generals Itakh and Wasif, and a few others, assembled to determine his successor. Ibn al-Zayyat initially proposed al-Wathiq's son Muhammad (the future caliph al-Muhtadi), but due to his youth he was passed over, and instead the council chose al-Wathiq's 26-year-old half-brother Ja'far, who became the caliph al-Mutawakkil.
This selection is commonly considered by historians to have been in effect a conspiracy to place a weak and pliable ruler on the throne, while the same cabal of officials would run affairs as under al-Wathiq. They would be quickly proven wrong, for al-Mutawakkil quickly moved to eliminate Ibn al-Zayyat and Itakh and consolidate his own authority.
Al-Wathiq is reported as having been generous to the poor of the holy cities of Mecca and Medina, and to have reduced taxes on maritime commerce, but he does not appear to have enjoyed any great popularity. What is told of his character shows him being a mild-mannered person, given to indolence and the pleasures of court life, to the point of becoming inebriated and falling asleep. He was an accomplished poet — more poems of his survive than of any other Abbasid caliph — as well as a skilled composer. He also could play the oud well. Al-Wathiq was also a patron of poets, singers and musicians, inviting them to the palace. He showed particular favor to the musician Ishaq al-Mawsili, the singer Mukhariq, and the poet al-Dahhak al-Bahili, known as al-Khali (lit. 'the Debauched One').
In contrast to this picture, the 10th-century historian al-Mas'udi portrays al-Wathiq as "interested in scientific learning and facilitating disputations among physicians". The Graeco-Arabic translation movement continued to flourish under his reign, and the sources also relate some episodes that show al-Wathiq's own "intellectual curiosity", especially as related to issues that could burnish his religious credentials: 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 the chancery official Sallam al-Tarjuman 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.
Al-Wathiq is one of the more obscure Abbasid caliphs. Al-Wathiq had several concubines. The most famous of them was Qurb, also known as Umm Muhammad. In 833, she gave birth to al-Wathiq's elder son, Muhammad, the future caliph al-Muhtadi. Another known and famous concubine was Faridah, who was also a musician and al-Wathiq's favorite. When al-Wathiq died, the singer Amr ibn Banah presented her to Caliph al-Mutawakkil. He married her, and she became one of his favorites.