Police received a report shortly before 12.45pm yesterday that a boat carrying two workmen had overturned on the river at Thwaite Gate, Hunslet.
A spokesman said: "Emergency services attended the scene and one of the men was rescued from the water and was taken to Leeds General Infirmary in a serious condition.
"The other man was accounted for nearby and was taken to hospital suffering the effects of shock and hypothermia."
A crime scene was put in place while the circumstances were investigated.
The Health and Safety Executive has been notified.