The waterman was on the river near Bad Oeynhausen when he found the infant corpse in a canal, a police spokesperson said.
The corpse showed injuries that may have been caused by an animal, and an autopsy on Friday will determine whether the child survived birth and the cause of death.
The homicide division has opened an investigation in to the infant's death.
Germany has been plagued with gruesome infanticide cases in the last few years. One woman who killed nine of her babies was sentenced to 15 years in prison in early April.