When Bosnia and Herzegovina declared independence from Yugoslavia on 3 March 1992, the response from the Serb-dominated Yugoslav People's Army was swift. In Mostar, JNA artillery attacks on the suburbs began on 6 April, and over the following weeks the army -- 17,000 soldiers strong -- gradually established control over large portions of the city. The Croatian Defence Council and the Army of Bosnia and Herzegovina fought side by side against the common enemy. The JNA shelling was devastating: the Catholic Cathedral, the Franciscan Church and Monastery, the Bishop's Palace with its library of 50,000 books, twelve of fourteen mosques, the historical museum, and the city archives were all damaged or destroyed. Every bridge across the Neretva was destroyed except one -- the 16th-century Stari Most. About 90,000 residents fled. In June, Operation Jackal, launched by Croatian Army forces advancing from the south, broke the encirclement. By 21 June the Yugoslav forces had been pushed out of the city entirely.

The alliance that liberated Mostar did not survive the liberation. The political landscape had been shifting since the previous year, when Croatian President Franjo Tudjman and Serbian President Slobodan Milosevic had reportedly discussed partitioning Bosnia and Herzegovina between them. The Croatian Community of Herzeg-Bosnia, declared in late 1991 with Mostar as its capital, increasingly acted as an independent entity -- its own police, currency, and school curriculum, all exclusively Croatian. Mate Boban, its president, blocked arms deliveries to the Bosnian government and began purging Bosniaks from the HVO. By mid-April 1993, Mostar was effectively a divided city. The western half was controlled by Croatian forces. The eastern half, where the Bosniak population was concentrated, was about to become a trap.

Between June 1993 and April 1994, the HVO besieged East Mostar. The International Criminal Tribunal for the former Yugoslavia documented what followed in precise, devastating language: "intense and uninterrupted gunfire and shelling" that killed many civilians, the destruction or severe damage of ten mosques, and the near-complete cutoff of humanitarian aid. The Bosniak population was "forced to live in extremely harsh conditions, deprived of food, water, electricity and adequate care." Over 100,000 shells fell on East Mostar during the siege. The HVO expelled Bosniaks from areas it controlled in western Mostar, sending men to detention camps at Dretelj, Heliodrom, Gabela, and Ljubuski where prisoners were starved, tortured, and killed. Women, including at least one sixteen-year-old girl, were raped by HVO soldiers before being forced across the front line. The ARBiH also held Croat prisoners in poor conditions at facilities in Potoci and elsewhere.

By November 1993, the Stari Most was the last crossing between the two banks of the Neretva, used by the ARBiH for military supply and by civilians as their only means of moving between the divided halves of the city. On 8 November, an HVO tank began firing directly at the 427-year-old structure. The bridge collapsed into the river on 9 November. When President Tudjman asked Herzeg-Bosnia's leadership who had destroyed it, Boban claimed it had "collapsed on its own" from previous damage and heavy rain. Croatian state television blamed the Bosniaks. The ICTY concluded the bridge was a legitimate military target given its military use, but that its destruction caused disproportionate harm to the Bosniak civilian population. Its loss put the Bosniak enclave of Donja Mahala, on the west bank, into virtually total isolation.

The Washington Agreement of March 1994, brokered under heavy American pressure, ended the Croat-Bosniak War and established a federation between the two groups. But the agreement froze the ethnic division it was meant to heal. Before the war, Mostar's population had been roughly equal parts Bosniak, Croat, and Serb. Afterward, the pre-war diversity was gone. Municipalities with Croat majorities became entirely Croat; Bosniak-majority areas became entirely Bosniak. East Mostar absorbed over 30,000 displaced Bosniaks from other fallen towns. In western Mostar, evidence pointed to a deliberate Croatian resettlement program. Roughly 60 to 75 percent of buildings in east Mostar were destroyed or severely damaged, compared to 20 percent in the west. The city came under EU administration for an interim period meant to reintegrate it as "a single, self-sustaining and multi-ethnic administration." Three decades later, that project remains unfinished.