Police said they recovered the bodies of a 43-year-old man and his son, aged 19, in the Cooper Bridge area of Huddersfield last night.
The pair, who have not been named, had left their home in Pudsey early yesterday morning to go magnet fishing.
West Yorkshire Police said they were alerted at 11.18am when personal items including a jacket and car keys were found by the water side.
They then visited an address in Pudsey where a woman confirmed that her husband and son had left home to go fishing.
A search was launched and an underwater team recovered their bodies at around 7.20pm.
A West Yorkshire Police spokesman said: "At the moment the exact circumstances are unknown."
Witness are asked to call police on 101 with the log number 740 of June 16.