The Cologne Transport Service (KVB) said that if Rhine River water level peaked, the stability of the building site at the Heumarkt U-Bahn station in the city centre could be threatened.
But officials believe that if the excavation pit were filled with water, it would counter the pressure building up from outside.
KVB spokesman Franz-Wolf Ramien told broadcaster WDR on Monday that authorities were therefore building a separation wall between the Rathaus and Heumarkt station construction areas in preparation for emergency flooding.
The wall is meant to hold the water at Heumarkt and stop it from flowing further into the Rathaus station construction stage, in the event that a controlled flooding is necessary.
The announcement came as hundreds of thousands of people gathered in Cologne to celebrate Karneval.
It also followed numerous reports of shoddy building practices on the underground rail system.
Investigators into the deadly March 3, 2009 collapse of the city's historic archive building believe contractors cut corners on the supporting walls of the metro tunnel not only near the construction site near Waidmarkt, but also near the Rathaus and Heumarkt stations.
An additional 28 falsified records for underground metro construction at various sites across the city have been discovered, pointing towards organised crime, an investigation insider told daily Kölner Stadt-Anzeiger on Monday.
“We assume that it could be significantly more,” the source said. “For us it looks like systematic falsification.”
Over the weekend the paper reported fresh claims that shoddy work practices caused the collapse of the archive building, including a report that construction firms were skimping on concrete.