Officers were called to Egremont Promenade, Wallasey, shortly before 14:00 GMT on Friday after the body was spotted close to the shore.
Police are appealing for help in identifying the man, thought to be in his mid to late 50s.
He was described by police as white, of slim build with grey to ginger hair.
The death of a man whose body was recovered from the River Mersey is being treated as "unexplained" by police.