HRW said it had visited the war-torn city and interviewed the residents and activists who found the bodies, a forensics expert and 18 of the bereaved families.
The New York-based watchdog also reviewed 350 photographs and videos of the victims as part of their investigation.
"Many of the victims bore signs of having been detained and then executed, such as hands tied behind their back, gunshot wounds to their head, and tape across their mouth," the report said.
HRW said that it has yet to finish its investigation into who carried out the killings.
"The bodies floating down Aleppo's river tell a grisly tale," HRW researcher Ole Solvang said.
"It's hard to see how 147 people could have been executed and their bodies flung in the river in government-controlled territory, as the evidence indicates, without the knowledge of government forces operating in the area," he added.
"These executions underline the urgent need for objective and impartial investigations," Solvang said.
Activists in the area told HRW researchers that they had fished 230 bodies out of the river between January 29 and March 14, but the rights group itself was able to identify 147 victims, all male and aged between 11 and 64.
Aleppo has been the scene of intense fighting since terrorist al-Nusra Front and other militant groups seized a swathe of districts in July last year.
Since June 2012, militants completely blocked the occupied areas in Aleppo, letting no food or supplies enter the area.
There are daily reports of kidnapping, torturing and killing of residents in the besieged areas by the militants who usually post videos of their crimes on the internet.
Most of the families interviewed by Human Rights Watch insisted that, in many cases, the victims were merchants who did not cooperate with any armed groups.
In January, after the first bodies were found, the Syrian foreign ministry sent a report to the UN which said al-Qaeda loyalists of the al-Nusra Front carried out the killings.
The Syrian army is preparing to launch a major operation in Aleppo to free the occupied areas.