Durham Wildlife Trust is thinning trees from Milkwellburn Wood, just off the A694, in the Derwent Valley.
The charity has said the aim is to improve the nature reserve with a long term habitat restoration programme.
But some people who use the woodland, near Blackhall Mill, feel the work is harming the 200 acre site, which has a mixture of trees dating back hundreds of years and is home to various forms of wildlife.
Former forester Alan Platt, 56, of Beech Grove, Blackhall Mill, said it is ‘distressing’ for people to see hundreds of logs stacked up by footpaths.
He said: “It is really upsetting people and some have stopped walking in the wood because of it.
“It is a lovely wood and walking through the trees is just beautiful.
“But where the trees have been felled it is just becoming a boggy swamp. The sides are overgrown with bracken and brambles.”
Durham Wildlife Trust has said it is thinning several varieties of tree including Scots Pine, Norway Spruce, Western Hemlock and Japanese Larch as well as beech and sycamore.
Computer programmer Andrew Metty, 44, of Hamsterley, said: “They have used incredibly heavy machinery and nothing is going to grow where they have been working.”
Chris Jones, the charity’s living landscapes officer, said the work will restore the site back to a once expansive broadleaf woodland.
He said: “Gradually removing the conifers and non-native trees so that the native broadleaf woodland can re-establish across the site, will dramatically improve the area for wildlife.
“We work closely with the forestry contractors, in this case Euroforest, to ensure that all thinning is carried out as sensitively as possible.
“Despite these efforts it is inevitable that these thinning operations can seem harsh and destructive at first, particularly as the work has to take place in the autumn and winter months so not to disturb breeding wildlife. Nature quickly recovers and it doesn’t take long to start seeing an improvement in the biodiversity of these areas.”