Farmers made hay but rampant grass growth in 2016 made life hard for butterflies and even puffin chicks, according to a review of the year’s wildlife and weather by the National Trust.

The nation’s ever more variable weather brought both booms and busts, with brambles and birds doing well, and slugs flourishing. But bumblebees dipped and owls found field voles hard to find.

Farmers found a late spring and a gloomy June challenging, with disappointing grain harvests. But the second hottest September on record meant bringing in the crops was trouble-free, as well as leading to an autumn of spectacular colours in woodlands.

The National Trust is the country’s biggest farmer, with 2,000 tenants, the biggest landowner after the Forestry commission, and has conducted its annual review for a decade.

“In those 10 years, we’ve noticed pulses of unsettled weather become the norm,” said National Trust nature expert Matthew Oates. “We last enjoyed a good summer in 2006.” Winters have become generally milder and summers wetter, he said, which is in line with the trend anticipated by climate change scientists.

“Many species [are now] struggling in the face of climate change and more intensive farming practices,” Oates said. “Long term, changes in how we manage land have also led to wildlife declines – with more than half of species experiencing a drop in numbers in the last 50 years.”

A cold wet spring followed by mild and damp conditions in May and June resulted in extraordinary grass growth, which shot up a third faster than in previous years. This presented a feast for cattle and sheep, as well as boosting hay-making: the number of hay bales doubled at the Trust’s Packwood House in Warwickshire, for example.

But the rapidly rising grass also squeezed out the small plants on which many bees and butterflies rely. On the Purbeck peninsula in Dorset, marbled white butterfly numbers plummeted by 73% compared to 2015, while common blue butterflies fell 23%.

A marbled white butterfly. Lots of grass swamped smaller plants that butterflies feed on. Photograph: Ian Ward/National Trust Images

At Lytes Carey in Somerset, bumblebee numbers fell 85%, as the wildflowers in field margins were outgrown by grass. However, at nearby Collard Hill, careful grazing helped the large blue butterfly fare better.

Profuse grass growth also presented a problem for young puffins on the Farne Islands. “The wet spring meant that vegetation grew like mad and the poor pufflings struggled to make their way through the tall grasses out to sea,” said Gwen Potter, the National Trust’s countryside manager for the Northumberland coast.

The mild, humid conditions were ideal for flies though, which was good news for some birds, if not for farmers. “It was a bad summer for flies,” said Kath Birkinshaw, a sheep farmer at Ashes Farm in the Peak District, who said “fly strike” – maggots – had afflicted some flocks.

“But it was good for house martins. The birds never usually spend any time on the farm, but in mid-August 300-400 stayed a week on the farm,” she said. Flies like wet summers, as do slugs, which have plagued gardeners. However, wasps do not, with the National Trust reporting numbers crashing in many areas.

Also scarce were field voles, the favourite prey of barn owls. The voles go through three to four years of breeding boom and bust and 2016 appears to have been a deep trough, according to the National Trust, with no barn owl broods seen at Malham in the Yorkshire Dales or at Dyrham Park, near Bath.

Autumn was dry and mild, turning the leaves on trees into a kaleidoscope of colours, although topsy-turvy weather earlier in the year saw confused sycamore trees on the Dolmelynllyn estate in Snowdonia, shedding leaves in late July, after a hot spell in May was followed by a cold start to the summer.

Autumn – Keats’s season of “mellow fruitfulness” – is apple harvesting time and there were mixed fortunes in the orchards. In the south-east, a lack of rain led to smaller apples than usual, according to Alison Capper, chair of the National Farmers Union’s (NFU) horticulture board. But in the West Midlands, where Capper’s Worcestershire orchards are, and in Somerset, wet weather arrived just when needed.

“The rain came at a crucial moment late in the season, leaving us with lovely sweet and juicy apples,” said Rachel Brewer, cider maker at Barrington Court in Somerset. “There may be some sore heads in Somerset this winter: sweet apples means that our cider will be strong.”

Apples at Barrington Court, Somerset, where well-timed rain made this year’s crop juicy and sweet. Photograph: John Millar/National Trust Images

Dry conditions late in the year in the east also caused problems for arable farmers sowing crops for 2017. “For the chaps out east, we had a bit of drought,” said Tori Morgan, the NFU’s adviser on combinable crops. “There have been some problems with oilseed rape not germinating properly. It has been so dry there hasn’t been the moisture needed to get that kickstarted.”

Overall cereal harvests were well below average for barley and rape, and just under for wheat, all thanks to gloomy early summer weather. “There was a lack of light over June, so we did not get the grain fill needed,” said Morgan. The upside was that the smaller, dense grains were packed with the protein needed to meet top quality milling requirements, helping British farmers exploit a poor year in France.

Morgan agrees with the National Trust assessment that the weather is becoming more unsettled, noting that December has seen both very warm and cold weeks. “Variability is increasing and farmers have got to try to work out a way to manage that volatility in the weather,” she said.

Globally, 2016 will be the hottest year on record, but Capper is hoping for a proper winter. “What we really want now is a cold snap through January and February and then an early start to spring in March,” she said. “Fruit crops and hops like a good winter chill: it helps with vernalisation, ie it helps them shut down properly. That means they will start with renewed vigour.”