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.
Two newly hatched osprey chicks have been stolen by magpies in Cumbria.