The bodies were found shortly after 3pm yesterday in a stream of water near the Ashington estate in Dublin 7.
It is believed that the man, in his 30s, was the boy’s father, and that the young victim was around three years old.
Local councillor Brendan Carr said the victims were visiting family locally, and that the deaths appear to be as a result of a tragic accident.
“My understanding is that the young man was carrying his child and tried to take a short cut through this particular gap in the fence over to see his parents, and something horrific obviously seems to have happened,” he said.
“It seems like a very bad accident,” he told RTÉ News.
The bodies removed to the city morgue at around 6pm.
The State Pathologist has been notified and a post mortem is expected to take place today.
The stream of water runs alongside the Dublin to Sligo rail line.
Irish Rail had suspended its Maynooth and M3 Parkway services from Connolly to Clonsilla for a short period while gardaí investigated the scene, however the line reopened shortly after 4pm.