In 1786 the family moved to Blans, a village near the Alssund, where he enjoyed drawing pictures of the surrounding countryside, and taking sailing tours in his father's boat.

He, however, had his sights set on being accepted at the Royal Danish Academy of Art (Det Kongelige Danske Kunstakademi) in Copenhagen.

On 1 July 1810, he married E. Christine Rebecca Hyssing against his wishes, in order to 'legitimize' a son, Erling Carl Vilhelm Eckersberg, who had been born to her.

Along with Tønnes Christian Bruun de Neergaard, writer, enthusiastic art lover and financial supporter, he made his way through Germany to Paris.

He worked on improving his skills as a history painter, and enjoyed painting smaller studies of the local life and area.

He was admitted as a member of the Academy in October 1817, and was named professor there in 1818, having assumed the vacant professorship left after the death of Nikolaj Abraham Abildgaard in 1809.

A year after the death of his wife Elisabeth in 1827, he married her sister Susanne Henriette Emilie Juel, with whom he also had several children.

In spite of his abilities in this genre, his career in portraiture was short-lived, due to the competition he received from then popular Christian Albrecht Jensen.

The experience of sailing out on the open seas gave new dimension to his marine paintings, which until that point tended to be calm depictions.

The Admiralty in 1819 had granted him free access to the Copenhagen Naval Station (Holmen), thus giving him occasion to view the many ships – a favorite motive in his paintings.

This gave Eckersberg a unique opportunity to watch men in a state of complete undress and to make an artistic evaluation of their physical build.

He made a small number of etchings that combine observations of daily life with classical, harmonious principles of composition.