In 1896 Eberhardt transferred to the Black Sea Fleet, serving as gunnery officer on the battleships Ekaterina II and Chesma.

In 1898 he moved back to the Russian Far East; he commanded the cruiser Admiral Nakhimov and took part in suppressing the Boxer Rebellion of 1899-1901 in China.

During the Russo–Japanese War of 1904-1905 Eberhardt served as chief naval aide to Yevgeni Ivanovich Alekseyev, the Viceroy of the Russian Far East [ru] (in office: 1903-1904).

Eberhardt served as Chief of the Russian Naval General Staff from 1908 and as Commander-in-Chief of the Black Sea Fleet from 1911.

However, he showed reluctance to start further offensive actions against Ottoman positions in the Bosporus, and Aleksandr Kolchak succeeded him in June 1916.