The boy, believed to be nearly 12 months old, was pulled from the River Irwell, just before 4.30pm. The baby was rushed to hospital but died a short time later
A 22-year-old man has been arrested on suspicion of murder.
Get Supt Jamie Daniels said it was an “incredibly tragic accident” which “has led to an innocent baby boy losing his life”.
It was not clear how the boy came to be in the water, according to officers.
Unconfirmed reports suggest that the baby was thrown from a bridge.
Talking to the BBC, Enzo Cabuderra, a local restaurant worker in the area said he arrived to find police and ambulance staff at the scene.
He said: ”I’ve got grandkids myself and to think that someone could do something like this.
“It’s just shocking.”
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He said: “I know his loss will be felt by the entire community and our thoughts are very much with his loved ones this evening.
“A murder investigation is underway and we are working hard to piece together the circumstances that led to the baby boy ending up in the water.
“Whilst we have a man in custody, our investigation is ongoing and I’d urge any witnesses or anyone with any information to get in touch as soon as possible so that we can find out what happened to him.”
A spokeswoman for Greater Manchester Fire and Rescue service said crews “rescued one casualty who was then handed over to North West Ambulance Service.
“Fire engines from Whitefield, Farnworth and Eccles attended the incident along with a water incident unit from Eccles.
“Crews rescued one casualty who was then handed over to NWAS (North West Ambulance Service).”