The 12-month-old baby was recovered from the River Irwell in Radcliffe, Greater Manchester, shortly before 4.25pm yesterday.
He was rushed to hospital but died a short time later.
A 22-year-old man was arrested on suspicion of murder and remained in custody last night, said Greater Manchester Police.
It is understood officers are treating the matter as a domestic incident.
Detective Superintendent Jamie Daniels said: "This is an incredibly tragic incident that has led to an innocent baby boy losing his life and we are doing everything we can to support his family at this unimaginably devastating time.
"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 under way 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."
Greater Manchester Fire and Rescue Service said: "We were called at 4.28pm to a rescue of a person in water in Radcliffe.
"Crews rescued one casualty who was then handed over to North West Ambulance Service."