A statement by the waterways and shipping office, called Wasser- und Schifffahrtsamt Stralsund, said the work would be carried out in the Adlergrund area near the island of Ruegen.
It said anchoring or fishing in the area was not permitted and warned of measuring and demarcation buoys.
The Gazprom-led consortium building the 1,230 kilometre (km) pipeline said on Saturday that work would resume.
Work came to a halt a year ago and western finance partners stood back, but did not pull out, as long-standing U.S. opposition to the project accelerated and erupted into sanctions threats and, later, concrete sanctions provisions.
The pipeline will bring Siberian gas into the heart of Europe, where Germany will act as importer and onward shipper in a region that is attractive to gas suppliers from across the world, including the U.S., as its own resources are dwindling.
Several European Union countries have supported the U.S. stance, expressing concern the infrastructure could make Berlin too dependent on Russia for energy.
The resumption of activity comes after outgoing U.S. President Donald Trump, whose administration has staunchly opposed the pipeline, lost to President-elect Joe Biden in the Nov. 3 election.
A 120 km stretch still needs completing.
The western partners are Germany's Uniper, BASF's Wintershall Dea, Anglo-Dutch oil major Shell, Austria's OMV and Engie.
(Reporting by Vera Eckert, editing by Christoph Steitz and Bernadette Baum)