The police were called at around 5.55pm following the report of a concern for a person in the water.
A spokesperson said: “A multi-agency operation was launched and a body has been recovered from the river.
“Formal identification has still to take place but the family of a 13-year-old boy have been made aware.
“A report will be submitted to the Procurator Fiscal.”
The teenager was one of six people to drown in Scotland over the weekend, and one of two in South Lanarkshire,
A 11-year-old, named locally as Dean Irvine, got into difficulties while playing with friends at Alexander Hamilton Memorial Park in Stonehouse.
This followed the death of 16-year-old the death of 16-year-old Connor Markward at Balloch Country Park on Friday.
A 29-year-old woman, a 9-year-old boy and a 410year-old man also died on Saturday evening after getting into difficulty near Pulpit Rock at Loch Lomond.
Edina Olahova, her son Rana Haris Ali and family friend Mohammad Asim Raza lost their lives, while Mr Raza’s seven-year-old son was rushed to intensive care at the Royal Hospital for Children.
Clydedale MSP Màiri McAllan said: “This news is utterly heartbreaking. My love and prayers are with all those who’ve lost their loved ones - and with those still fighting for their life.
“Scotland’s waters are beautiful but with freezing temperatures and hidden currents they can be treacherous – please, please be careful.”
South Lanarkshire Council leader John Ross added: “The drowning deaths that took place over the weekend across Scotland are truly heart-breaking, and my thoughts are with all those affected by these tragedies.
"It was particularly awful to learn that two children had lost their lives in incidents in South Lanarkshire and I know everyone will join me in sending my sincere condolences to the families devastated by these deaths.
“Our area is renowned for its beauty spots, including areas with rivers, lochs and reservoirs, but everyone needs to be aware that where there is water there is danger.
"It’s proving to be a hot summer and it may be tempting to go for a swim or paddle, but conditions can change quickly for even a strong and experienced swimmer. So think twice, and the safest thing to do may be to simply stay out of the water.”
The police urge people to “exercise extreme caution” when swimming in open water.
Assistant Chief Constable Mark Williams said: "The number of deaths in open water this weekend is hard to comprehend and my thoughts are with the families and loved ones of those affected.
"The message I want to send to everyone is exercise extreme caution. It is better to keep a safe distance from water if possible.
"Tragically, this weekend has highlighted that open water is very, very dangerous. If you see someone in the water and distressed call 999 immediately.
"Remember, you could get into difficulty yourself trying to help so please take care and seek help as soon as possible."