During the 19^th century, the Great Cormorant was exterminated as a breeding bird in several Baltic countries. The persecution continued until the mid of the 20^th century, and in the early 1960s the European breeding population of the continental subspecies sinensis had declined to 4,000 breeding pairs (bp) only, of which Germany and Poland hosted more than the half. During the following two decades, the population development apparently has also been affected by the harmful effects of DDT and PCB.

As a result of protection measures, and seemingly also due to the ban of DDT and PCB, breeding pair numbers started to increase during the second half of the 1970s. During the 1980s, the Cormorant started to expand its range towards the northern and eastern parts of the Baltic. Currently, the species is present in the whole Baltic Sea area, including the northern parts of the Gulf of Bothnia.

Baltic-wide surveys in 2006, 2009 and 2012 showed that the Baltic population had stabilized at a level of 155,000 – 170,000 bp during that period. However, after 2012 breeding pair numbers have still increased in the eastern and northern Baltic. Hence, the current population is estimated at 190,000-210,000 bp.

The highest population densities are found around the highly eutrophic estuaries of the southern Baltic (Odra-, Vistula-, and Curonian lagoon).