The observatory's first director, Karl Friedrich Knorre, arrived on the recommendation of the great astronomer Vasily Struve and then never really left, holding the post for fifty years. Alongside training naval officers, Knorre pursued real research, and he is remembered in the history of astronomy as the author of one sheet of the Berlin Academy's star map, a chart so accurate that other astronomers used it to identify the minor planets Astraea and Flora against the fixed background of stars. His successor, Ivan Kortazzi, catalogued a band of the sky that came to be called the Nikolaev Zone. In these marine decades, both men also went to sea, surveying the coasts and pinning down the exact coordinates of countless points on the maps of the Azov, Black, and Marmara Seas, work on which lives depended.

From 1912 the observatory became a southern branch of the famous Pulkovo Observatory, and its task expanded to extending Pulkovo's great star catalogues into the southern sky. What followed was a test not of instruments but of endurance. The institution survived the First World War, the Russian Revolution, and the Civil War as a working scientific body, held together by directors who refused to let it collapse. In 1931 it created a highly accurate Time Service that fed national and international efforts to pin down the exact hour. During the Second World War the observatory was under German occupation from 1941 to 1944, and its director managed to shepherd it through without serious destruction, an achievement that let the science resume almost as soon as the war ended.

In the postwar decades the observatory received precision instruments from Pulkovo, including a meridian circle and a zonal astrograph from the Carl Zeiss firm, and its photographic observations of solar system bodies became among the most accurate in the world. It tracked the first artificial satellites, mounted expeditions to the Caucasus and the Arctic island of Spitsbergen, and produced roughly thirty-five separate catalogues of celestial positions. In 1992 it became an independent institution, and it has since built automated telescopes with electronic detectors, a Fast Robotic Telescope, and in 2009 Ukraine's first mobile telescope. Protected as a heritage building since 1963, the observatory on Spassky Hill remains what it has always been, a place where the patient measurement of stars serves the very real business of knowing exactly where and when we are.