A logistics concept that found recognition the world over was developed and implemented for the millions of cubic metres of soil and building materials in the project. Material was supplied and removed by inland waterway, rail and road transport. Over 80 percent of the debris removed from the old Lehrter Stadtbahnhof was transported to the waste disposal plant by barge.

For transport to the construction sites, the project had its own road network to avoid emissions, traffic noise and loads on public roads. The groundwater was constantly monitored by computer. The groundwater management system ensured that Berlin's subsoil conditions remained stable – good for the Tiergarten park and good for the numerous old buildings that have traditionally been built on oak piles.

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Up to 100 measuring points checked the groundwater levels every hour over an area of four square kilometres in the centre of Berlin. The data were transmitted automatically by radio to the groundwater management computer centre, whose computers compared the measured values with the levels specified by the authorities. In the event of deviations, groundwater was either pumped out of the respective excavation pits, cleaned and, with iron and manganese removed, transferred to draining wells, or pumped into the River Spree.