Whatever the truth, the killings added to an atmosphere of despair as the UN and Arab League envoy arrived in New York to brief the Security Council.
Diplomats at UN headquarters said Brahimi had reported that he had made "no progress" in efforts to establish talks on a political transition in a country where 22 months of war have left more than 60,000 dead.
"The tragedy does not have an end," Brahimi said, adding that Assad's legitimacy has been "irreparably damaged" but warning that the regime could still cling to power and perpetuate the bloodshed indefinitely.
"I'm sorry if I sound like an old broken record," he added, according to diplomats. "The country is breaking up before everyone's eyes. Only the international community can help, and first and foremost the Security Council."
Assad's forces have become more repressive, the veteran troubleshooter and former Algerian foreign minister was quoted as saying, but he insisted both the state and the rebel opposition are committing "equally atrocious crimes."
Brahimi told the council he was very worried about countries around Syria, which face a growing risk of "contamination" from the conflict.
"Most regional parties have aligned with one of the parties in Syria," Brahimi said. "There might be implications if the crisis continues spiraling. The refugee flow is becoming a matter of controversy in these countries."
"Syria is becoming a playground for competing forces," he declared. "None of the neighbors is immune to the fallout consequences of the conflict. The region is facing the risk of contamination."
The Security Council has been paralyzed on Syria for more than a year. Russia and China have vetoed three western-drafted resolutions which would simply have threatened sanctions.
Russia accuses the West of seeking regime change through force and insists it cannot make Assad stand down. The United States and its allies back the opposition stance that there can be no talks with Assad.
In the war-ravaged Syrian city of Aleppo, rebel fighter Abu Seif said the 78 bodies had been retrieved from the Quweiq River and that 30 more were still in the water but out of reach because of the threat of regime snipers.
The scene on the banks of the Quweiq was grim, as muddied corpses were dredged out and hundreds of distressed people flocked around to see if they could spot among the bodies a father, a brother, a son or a husband.
"The regime threw them into the river so that they would arrive in an area under our control, so the people would think we killed them," Abu Seif said.
But a government security official blamed "terrorists" -- the regime term for the rebels -- for the killings, saying the victims were residents kidnapped from the opposition-held district of Bustan al-Qasr.
There was no immediate claim of responsibility, but the official SANA news agency said the jihadist Al-Nusra Front carried out the executions.
Al-Nusra, which first gained notoriety for its suicide bombings in Syria, has evolved into a formidable fighting force, leading rebel attacks throughout the embattled country.
Its suspected affiliation to the Al-Qaeda offshoot in Iraq have seen it added to the US list of terrorist organisations.
"My brother disappeared weeks ago when he was crossing the regime-held zone, and we don't know where he is or what became of him," said Mohammed Abdel Aziz.
Volunteers heaped bodies on a truck. An AFP correspondent counted at least 15. They were then taken to a school where they were laid out and covered.
"We do not know who they are. They were not carrying papers," a volunteer said.
A number was placed next to each body and their faces were left uncovered to allow identification by relatives at the school, where the nauseating stench of death lingered.
"There are those who drowned because they were shot in the legs or abdomen before being thrown into the water," said a nurse, noting some may have been killed up to three days ago.
On the eve of a donors' conference in Kuwait, charity organisations pledged $182 million (136 million euros) for Syrians displaced or driven abroad.
US President Barack Obama announced an extra $155 million to aid refugees fleeing what he said was "barbarism" propagated by Assad's government.