It happened just after 6 a.m. on the New Jersey River Line Light Rail track near US 130.
The train was traveling southbound from Trenton when it struck a tree just north of Roebling Station.
The train operator was killed, according to officials. The name of the operator has not yet been released to the public.
The train had 42 customers on board at the time of the incident. Of the passengers, 23 sustained non-life-threatening injuries, which are said to be mostly minor. The other 19 were accommodated by a bus.
Chopper 6 was overhead, where a large piece of a tree could be seen under the front of the train.
People could also be seen being removed from the scene on stretchers.
NJ Transit River Line is suspended in both directions between Florence and Trenton.
Action News spoke with people who live nearby, who said they've never seen anything like this.
"We've never heard of an accident since the beginning. We've been here for about 40 years and we never heard of an accident with the River Line," a nearby neighbor said.
People who live near the tracks say falling trees are a common problem.
"It's a recipe for disaster," said Patrick Reding of the dozens of trees that separate his home from the tracks.
He says it's something he often worries about after part of a tree fell on his property, causing damage.
"We get a lot of high winds here because we're exposed here, and it caved in the roof of my pickup," Reding said.
There is a staging area for the families of those injured at the River Front Motel.
New Jersey Transit Police are on scene and investigating.