Usually underground works compared to the surface alternative, minimise the negative impact caused to the surface fauna and flora. As a matter of fact as the impacts are proportional to the occupied surface area, it is clear that an underground rail or road will have less impact as the same one build at the surface.
The construction of a tunnel in a mountainous zone could have negative impacts, of course much less as if built in surface. The main indirect effect is due to the fact that the tunnel will bring human activities in an isolated zone and therefore produce negative impact on the fauna and flora. For a road tunnel, ventilation coul emit polluted air which will have an impact. During the construction a depression of the groundwater table could have an impact on the fauna and flora nearby.
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