Many plantings were done "by unqualified employees with large-scale violations" of methodology, the environment ministry watchdog said in a court decision last year, adding that tens of thousands of rare trees that were planted as compensation were "irreparably lost."
Moreover, certain reptiles and brown bears are no longer present in the area around the mountain venues, according to official reports by Sochi National Park.
Another hotly contested issue is the fate of the Mzymta, Sochi's largest river, which flows from a lake in a Caucasus reserve down to the Black Sea.
'The river is the biggest shame'
A road and a railway were built along its undeveloped left bank, connecting Sochi's airport with Olympic skiing venues upstream.
Of the damage done to Sochi's wilderness, "the river is the biggest shame," said Igor Chestin, head of WWF in Russia.
The river is the spawning site of one-fifth of Russia's valuable Black Sea salmon.
"Its value as a fishery has been lost due to the change of the shape of the river, and years of pollution" since Sochi was picked as the 2014 Winter Olympics host in 2007, Chestin said.
Geologist Yevgeny Vitishko, another activist with Environmental Watch, said the rugged topography of the area had required a system of tunnels and bridges for the road and rail network. "About 15 years" would have been needed for proper study and building, he told AFP.
During the years of preparation, the Games organizers released millions of trout hatchlings into the river in several batches.
But an official monitoring report last year found no evidence that any of the fish had survived.
It said much of the Mzymta had been transformed from a clean, white-water river into a controlled waterway, tainted by chemical pollutants and debris.
Russian officials have brushed aside most of the criticism. Deputy Environment Minister Rinat Gizatulin recently advised green activists to "stop tying themselves to every tree" in Sochi and instead appreciate the new gas-fired heating plant and sewage treatment facilities.
Meanwhile activists Gazaryan and Vitishko have both been made to feel the force of the law after being convicted for property damage following a protest over a residence allegedly belonging to the local governor.
Gazaryan, who spoke to AFP from Tallinn, has since claimed asylum in Estonia. Vitishko was ordered to serve a three-year sentence in a penal colony and is currently free pending appeal.