A chicks' mother and father had returned to the nest in Bassenthwaite at Easter for the fourth year running, producing a trio of eggs in six days.
The first of the three chicks hatched on Thursday, with the other two birds arriving over the weekend.
But the Lake District Osprey Project said Monday was a "sad day", when the team saw only one chick was on the nest.
A spokesman said it was a "bleak" outlook for the remaining chick as it is "very likely" that the magpies would return.
It is not known if the birds, which often take scraps of fish from the osprey's nest, had eaten the chicks.
Ospreys returned to the area in 2001 after an absence of more than 150 years, and nearly 30 chicks have been raised at the nest since.
The birds fly south to Africa during late autumn, returning to the UK towards the start of April.

The source close to the inquiry played down the significance of the interviews carried out in Portugal on Tuesday.
Portuguese detectives in Faro were observed during the questioning by officers from the Met Police, which is conducting its own investigation.
Madeleine disappeared aged three in the Algarve resort of Praia da Luz in 2007.
The source told the BBC: "Questioning of the four suspects was concluded yesterday evening. Unfortunately the interviews have led to no new developments and we are back where we were seven years ago."
The source added: "The 'arguido' [suspect] status was given to the suspects to protect them. It gives them legal rights including the right to remain silent and to have a lawyer present during interviews.
Jeremy Cooke, BBC News in Praia da Luz
It is clear that the latest developments in the Madeleine McCann case are the result of the detailed, painstaking work being done by British police officers working on Operation Grange.
As their investigation continues, they formally request assistance from the Portuguese police. It is at the request of Scotland Yard officers that four potential new suspects - or arguidos - and 11 potential witnesses are being interviewed.
Those interviews involve detectives from both countries; the Portuguese asking the questions, while the British monitor proceedings.
It is not clear what potential link the British team believe may exist between the "suspects" and the disappearance of the three year-old. But clearly there are lines of inquiry they believe are worth following up.
There are, however, clear tensions here. With one source close to the case saying that the investigation is going nowhere and "we are back where we were seven years ago".
"They were declared arguido due to being identified as suspects in a letter of international request sent by the British to the Portuguese authorities."
The Portuguese Attorney General's Office in Lisbon issued a brief statement about the questioning of the four suspects.
It said that requests from the British authorities had been carried out but the content of these requests would remain confidential.
Police have begun the process of interviewing 11 witnesses, which also relates to official requests from the Metropolitan Police.
The source indicated that two tracker dogs from the UK could be used in searching a vehicle thought to belong to one of the witnesses. No time or location was given for this.
One of the four "persons of interest" - or arguidos - questioned was Sergey Malinka. He has always denied any involvement.
Mr Malinka, a Russian-born website designer with Portuguese nationality, was questioned as a witness in 2007 when Madeleine went missing.
On Tuesday, Mr Malinka and another suspect left the central police station in Faro after they were interviewed.
A third person, who is said to be suffering from severe schizophrenia, remained inside the police headquarters after the other two had left.
All of those being questioned are Portuguese citizens. They have all been summoned to be interviewed; there have been no arrests.
The status of arguidos in the Portuguese judicial system refers to individuals whom police may reasonably suspect are linked to a crime.
In June, Portuguese and British officers searched three sites in Praia da Luz but found no evidence relating to the case.
Scotland Yard said at the time that "more activity" had been agreed with Portuguese police and the searches were the "first phase" of a major investigation.
The McCann family - from Rothley, Leicestershire - were staying in an apartment in Praia da Luz when Madeleine was last seen.
Her parents had been at a restaurant near their apartment when she went missing.
Two newly hatched osprey chicks have been stolen by magpies in Cumbria.
[NEXT_CONCEPT]
Questioning of four suspects in the Madeleine McCann investigation has concluded without any new developments, a source has told the BBC.