Two chimneys at the Lafarge Cement works, the tallest of which was 550ft, came down in March last year marking the end of nearly 200 years of cement production.
Lafarge is currently restoring rail sidings at the site, which are expected to be operational from February next year.
The first main user of the line will be Crossrail, which is providing a £16bn rail scheme linking the Thames Gateway and the Thames Valley, from Abbey Wood and Shenfield in the East to Heathrow and Maidenhead in the West.
Crossrail will use the new line to transport excavated material from its western tunnels at Royal Oak, near Paddington, by train to Northfleet.
The material will then be sent to a RSPB nature reserve at Wallasea Island in Essex by ship.
Chairman of the Rail Freight Group, Lord Tony Berkeley, visited the site to see the £13.5m rail investment project.
Commenting on progress work, Lord Berkeley, said: "The availability of Lafarge’s Northfleet site means Crossrail can keep the movement of excavated material from the Royal Oak tunnelling site off London’s roads while also contributing towards the creation of a major new RSPB nature reserve.
"It was exciting to see such a large-scale engineering project being delivered with sustainability at its heart."