Kargbo said authorities had discovered 60 bodies on the shore and one survivor, a week after the city was struck.
"I would advise not to go and start to swim until we feel it is safe and reasonable enough," Yassin Kargbo, the director general of the city's tourism office, told reporters in Freetown.
He said the city put out the advisory "because of the different debris that came into the water and the likelihood that you (could) get yourself hurt or contaminated by the water".
Kargbo said authorities had discovered 60 bodies on the shore and one survivor, a week after the city was struck by flooding and mudslides that killed nearly 500 people.
At least 600 others are also still listed as missing, according to the Red Cross.
Guinean authorities found three bodies this weekend on the shores of Kaback, a town about 30 kilometres (18 miles) from the northern Sierra Leonean border.
The disaster struck on August 14 after Freetown, home to 1.2 million people and the capital of one of the world's poorest countries, had been pounded for three days by torrential rain.
According to the charity Save the Children, the disaster killed 122 children and left 123 orphaned.
Authorities in Sierra Leona have been burying unclaimed bodies in mass graves for the past week in a rush to avoid water-borne diseases such as cholera -- which are a major fear and another reason the country is telling people to stay away from the capital's beaches.
"Most of the debris have been removed," Kargbo said, including palm trees and building materials lying along the beach.
"You can come and have fun," he added, "but I would advise against swimming. The water is still full of mud and other particles that were washed into the sea".
"And you will also notice the smell".