The incident took place at around midnight yesterday near Bakolibari when a family of three were travelling in the boat from their native village of Burgaon to Mayong primary health centre.
Joydeb Biswas (42) and his nine-year-old son Papa Biswas went missing in the water while Joydeb's wife was rescued by the local people after they heard some screams.
A search operation has been launched for the missing duo who remain untraced till the time of filing of the report.