Approximately one hectare of ancient woodland will be lost in the Mid Colne Valley. One of the two breeding sites for the pochard duck for in this area will be lost, and corn bunting habitat will be lost from farmland between the M25 and the A412 Denham Way/North Orbital Road.
The 3.4km Colne Valley Viaduct over the Mid Colne Valley SSSI will have a 3m high noise barrier along part of the western edge. The Colne Valley HS2 Community Forum had requested that a tunnel be constructed to pass beneath the lakes between Ruislip and the M25 but this was rejected as it would also require the extension of the Chiltern tunnel southwards. The entrance to the tunnel is in a cutting and will have a porous portal – a perforated concrete box that extends out from the tunnel entrance to reduce noise and ease air pressure changes. Half a hectare of hardstand will be provided for maintenance and emergency access.