The preserve was initially established on July 14, 1927 as part of the Trans-Maritime Preserve by the decree No. 172 of the Council of People's Commissars of Ukrainian SSR. In 1933 the preserve became an independent research institution. In 1973 to the Black Sea Preserve were added the Danube floodplains, Kinski islands in Yahorlyk Bay, and the shallow portion of the Gulf of Tendra. Next year the neighboring Yahorlyk reserve was annexed as well. In 1981 the Danube floodplains became an independent preserve. In 1983 there was established the Black Sea Biosphere Reserve that included the Black Sea State Preserve and the Yahorlyk State Ornithological Reserve (as its buffer zone). In December 1984 the reserve was accepted to the World Network of Biosphere Reserves. The territory of the preserve is included into the International list of Ramsar Convention.