The Black Sea is a 2200 m deep anoxic, marine sea connected to the Mediterranean Sea via the Dardanelles Strait, Marmara Sea, and the 3 km wide, 35 m deep Bosphorus Strait. The biogeochemistry of sediment from the Anatolia slope has recorded changes to the hydrography leading up to and following the input of Mediterranean water at ~9.4 ka (103 years B.P.), when global sea level rose to the level of the Bosphorus sill and high‐salinity water from the Mediterranean began to spill into the then brackish lake. The water initially mixed little with the lake water but cascaded to the bottom where it remained essentially isolated for ~1.6 kyr, the time required to fill the basin from the bottom up at its present input rate. The accumulation of Mo in the seafloor sediments, a proxy of bottom‐water anoxia, increased sharply at ~8.6 ka, when bacterial respiration in the bottom water advanced to SO42− reduction by the oxidation of organic detritus that settled out of the photic zone. Its accumulation remained elevated to ~5.6 ka, when it decreased 60%, only to again increase slightly at ~2.0 ka. The accumulation of Corg, a proxy of primary productivity, increased threefold to fourfold at ~7.8 ka, when upward mixing of the high‐salinity bottom water replaced the then thin veneer of the brackish photic zone in less than 50 years. From that time onward, the accumulation of Corg, Mo, and additional trace metals has reflected the hydrography of the basin and Bosphorus Strait, controlled largely by climate.