The target of the, as yet, unknown thieves was the heavily guarded building site in Berlin, which had experienced several setbacks since its construction began nine years ago.
The massive leak was caused by burglars who removed water taps from bathrooms on the fourth, fifth and sixth floors in a corridor leading to the main part of the complex. According to media reports, the damage was estimated at millions of euros.
A spokeswoman for the federal construction agency which manages the building site only confirmed the theft while the BND refused to comment on the situation.
The actual cost of the taps have been put at just a few hundred euros, clouding the actual motives for the crime.
The building site of the HQ is protected by a private security firm and monitored by dozens of security cameras. German media called the incident another embarrassment for the country's spy chiefs with Berlin's daily Tagesspiegel headline "Watergate at the new BND building."
The current headquarter of the BND is in Bavaria. The move to Berlin with some 3,000 staff members has been much delayed and now is scheduled for 2017.
In 2011, the blueprints for the new complex were stolen although the security risks posed by the loss were minimized.