Eyewitnesses say two boys were seen running away from the area.
The Buffalo Bayou Partnership operates the boats, and they say this came at a really bad time.
"This is kind of peak time for us to our organization," said Trudi Smith with the Buffalo Bayou Partnership. "To be able to offer these rides along Buffalo Bayou and it's a great way to experience this, but we are basically having to start over, start from scratch."
Officials also had to fish some equipment out that was dumped into the water. The vandalism is being treated as an arson case. There have been no arrests so far.