Ornithologists and landowners are reporting problems for the capercaillie, one of Scotland's most endangered birds, as well as black and red grouse and popular garden birds. Many puffins are feared to have drowned in their burrows.
Wildlife experts say many butterflies have suffered from the prolonged rainy spells, along with other insect species.
Vets are blaming persistent damp conditions for cattle contracting more potentially fatal diseases.
The Royal Society for the Protection of Birds (RSPB) reported that capercaillie and black grouse have had a particularly bad year.
"The chicks of these species have no ability to thermally regulate until they are about 10 days to two weeks old," said the RSPB Scotland's James Reynolds.
"If they get persistently wet during this time, then their mortality is increased significantly. We think this is what might have happened this year."
According to Reynolds, every forest estate the RSPB has talked to has reported that hardly any chicks have survived. "Weather conditions over-arch everything else," he told the Sunday Herald. "We can get the habitat right with the correct cover and trees planted, and remove fences to prevent lethal collisions, but ultimately if the weather conditions aren't right, then the birds can take a big hit at breeding and fledging time."
As the red grouse shooting season opened last week, the RSPB's fears were underscored by the British Association for Shooting & Conservation. It complained that the bad weather had made this year's prospects look poor.
The National Trust said that the dreadful summer had been "almost apocalyptic" for birds. Nine out of every 10 puffin burrows on the Farne Islands off the coast of Northumbria have been lost to floods.
A UK survey of garden birds, the results of which were released last week, found that blackbirds, song thrushes, robins, swifts and house martins had been hit by the cold wet weather.
The numbers seen in gardens by 78,000 members of the public were significantly down in June this year, compared to 2011.
Experts pointed out that prolonged rain made it more difficult for some adult birds to find sufficient food for their chicks.
If they stayed away from their nests for longer, the chicks could also have been exposed to more damp, chilly conditions.
Although birds across much of the country had suffered, in the Outer Hebrides where the weather had been unusually fine, they had done well.
"We know that productivity for golden eagles, hen harriers and short-eared owls has been particularly high in this area," Reynolds added.
The Scottish Wildlife Trust (SWT) said butterflies had been badly hit. "The last three cold wet Ayrshire summers must have negatively affected our butterfly populations," said Gill Smart, SWT's reserve manager for the west of Scotland.
"They don't fly in dull weather so won't be available for mating. Rain will disrupt that too and probably wash eggs away or stop them developing."
She said butterfly populations had declined as a result. "We need a good summer to bring the numbers up again. I suppose it makes the availability of good habitat all the more important, giving more opportunity for butterfly survival."
Sir David Attenborough, president of the Butterfly Conservation group, has predicted that wet weather would cut butterfly populations.
"It has made life hard for butterflies and things could get worse unless conditions improve," he said.
Government vets have warned farmers to expect an increase in the fatal cattle disease blackleg because of heavy rain and flooding.
Scientists based at the Scottish Agricultural College have diagnosed the disease at its centres in Edinburgh, Perth, Ayr, Dumfries and St Boswells.
They blame the outbreaks, caused by bacteria, on persistent damp conditions.
"Cattle between six and 24 months old are particularly susceptible to this disease," Alwyn Jones, a veterinary investigation officer at St Boswells, told Scottish Farmer magazine.
"Affected cattle are often found dead, although occasionally they may be lame and have a swollen upper limb before they die."
Jones said blackleg outbreaks occur during the summer months. "Most bacteria prefer warmth, and at this time of year young stock are out to grass," he said.
"Any disturbance of soil in grazing areas could expose the spores and is considered to be a potent trigger factor.
"The difficult conditions this year, with high rainfall, have caused plenty of that. Some farms are known to be at particular risk."
Farmers' union NFU Scotland advised farmers to considervaccinating cattle against blackleg.
"If warmer, wetter summers are to become the norm, then it is probably worth those with cattle and sheep ensuring blackleg is part of their health plan discussions with their vet," said the union's Scottish president, Nigel Miller.