While birds and insects struggled, slugs and orchids did well throughout Britain "in our special places", said the charity.
Trust wildlife advisor Matthew Oates said: "This has been a highly polarised year, with wildlife in the places we look after doing either remarkably well or incredibly badly.
"In general, plants and slugs were the big winners and insects the big losers. But even in this wet summer some insects did surprisingly well, at least in a few places.
"Our wildlife, farmers, horticulturalists and rural tourism and recreation industries are all long overdue a good summer, having suffered poor ones since 2006.
"Surely we are due a good one next year?"
It was a spring of two halves said the trust, with the warmest March since 1910 and the implementation of drought orders across England followed by the wettest April on record.
The April downpour had a detrimental impact on fruit harvests in the autumn as the spring rains washed away the blossom resulting in a very bad year for English apples across the board and autumn fruits and berries such as sloes and holly berries.
It was a bad summer for the insect pollinators and even those flowers that were pollinated struggled to set fruit in the ongoing wet weather.
The one big winner in 2012 said the trust was the slug with reports of a giant Spanish super slug invading our back gardens. One impact of the damp conditions has been rapid grass growth with a knock on effect for smaller plants.
Orchids have also been big winners this year.