A police team recovered the body from the river near the Cap San Diego museum ship at the city's harbour front after the captain of a ferry noticed it on Thursday morning.
They cautioned that an immediate identification was not possible because the body had been in the water for a considerable amount of time.
But the ID card found on the body belonged to Kraus and the clothes also matched the description of those the football boss had been wearing when he went missing.
On Friday investigators will definitely confirm whether the body belongs to Kraus by matching the teeth with his dental records.
The 44-year-old father of two went missing 11 weeks ago after leaving a riverside bar in the city's port on a Saturday night after meeting colleagues.
He was supposed to take a taxi home, but appears to have later returned to the harbour area, where his mobile phone was last located.
Police have failed to track down the taxi driver who was supposed to drive Kraus home, nor do they have any idea why he might have returned to the harbour front.