Last year's breeding season was the worst in more than 20 years, according to some monitors. Torrential rain last summer and heavy snows this winter have made hunting difficult for owls while a key food source – the short-tailed field vole – is believed to be in decline.
Conservationists have reported worrying falls in the number of barn owl breeding pairs and new chicks, though no national statistics are available.
Geoff Sheppard, who observes 70 sites in west Galloway for the Raptor Study Group, said he found only 39 barn owl chicks last year – significantly down from the 150 to 200 average.
He said: "It has certainly been the worst year I have seen. I started in 1984 but increased the number of boxes in 1990. It has been the worse year since then.
"I went out in May and almost all sites were empty. There weren't even birds there, they had just gone. Usually this means the voles have just crashed and the adult birds are having to spend all their time looking for food. We had an awful summer and one thing barn owls do not like is wet. They literally get waterlogged and can't fly. They barely manage to stay alive, let alone breed."
David Anderson, conservation manager of the Trossachs National Park, told a similar story. He said: "We have had really poor breeding performances in the past three years. It has been abysmal to be honest. The barn owl population here went from 36 breeding pairs in the forest down to two.
"It is not just to do with low vole numbers; it is to do with severe weather in the winter. Owls very rarely cope with scarcity of food and deep snow."
Scotland's barn owl population has fluctuated between 386 and 600 breeding pairs in recent decades according to The Barn Owl Trust, though local conservationists suggest this number could be higher.
Its strength is strongly linked to the field vole population, which rises and falls on a three to four-year cycle. Professor Xavier Lambin of Aberdeen University said: "Most of Scotland is experiencing cyclical fluctuations in field voles, with three to four year peaks. It varies quite a lot across Scotland. It moves like a travelling wave, a ripple when you throw a stone in a pond."
"I think we are at the trough [of the cycle]. It has been extremely high two years ago and declining last year so that would make sense. But we don't want to be alarmist, they will come back for sure."
The Barn Owl Trust said it hoped a dry summer would help the population bounce back.
A spokesman for the Scottish Natural Heritage said it was aware of the declining vole population and suggested it was due to a rise in predators.
A spokesman added: "The snow cover in 2010 and 2011 actually helped voles, as they can breed under snow, but it hampered owls' hunting. The number of some other owls, such as short and long-eared owls, are also of concern, but there is often a lack of data – these birds are hard to study because they're secretive and nocturnal."