The child went missing almost eight weeks ago on her way back from buying sweets at a shop 200 yards from her family home in Huelva, the provincial capital near the border with Portugal.
The Spanish girl's parents had repeatedly said that they were convinced Mari Luz had been taken against her will on Jan 13 and the McCanns had included her image in a poster campaign to find their own daughter.
Last night the badly decomposed body was spotted in water next to a petrol station jetty around 6pm on Friday. Police identified the child from the clothes she was wearing and her parents were expected to carry out a formal identification last night.
A police spokesman said that an initial examination had shown the child had suffered a serious blow to the head but no formal cause of death was expected until an autopsy could be performed overnight.
Gerry and Kate McCann sent a message of support to Mari Luz's parents.
The McCanns, whose daughter Madeleine has been missing for more than 10 months, said they were "extremely saddened" by the news.
"It's an absolute tragedy for Mari Luz's family," said the McCanns' spokesman Clarence Mitchell last night.
"Gerry and Kate's thoughts and prayers are with them now and through the coming days.
"They had developed a sense of unity with Mari Luz's parents, although they had never spoken
directly, as both families were going through similar agonies."
Police sources said Mari Luz's body had on the same pink leotard and boots as the day she vanished. Her distraught parents Juan Jose Cortes, 34, a former professional footballer, and Irene Suarez were last night preparing to formally identifying the body.