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Brookmill Nature Reserve is part of a former railway embankment from Nunhead to Greenwich Park that was finally completed in 1888 and ran for the next 28 years but ceased to operate at the end of 1916 as a wartime economy measure. After the war the western section was re-routed to Lewisham while the remainder was formally abandoned. The site was left to its own devices until 1979 when Lewisham Council bought the freehold from British Rail.
The site lies on the Upper Chalk, although most of the site is composed of the artificial substrate used to build the embankment and consists of a short section of embankment with steep sides and a flat top. Evidence from the flora suggests that this to is calcareous. The site is largely enclosed and borders Brookmill Road on its eastern side with iron railings and two gates for access. The northern and southern side border private gardens while the western side borders active railway land. There are three ponds on the site all with different construction and a wooden shed situated just inside the northern gate on Brookmill Road that acts as a tool store. A path runs around the perimeter of the site, crossing the embankment via steps near the western end. Another path, a cul-de-sac, runs from the main path along the length of the flat top of the embankment.