The Black Sea is the largest and most studied anoxic basin in the modern world. Much of this research has focused on the redox structure of the water column, specifically on the driving forces behind variations in the position, stability, and structure of the oxic-anoxic interface (chemocline). However, none of these studies has been able to quantify the historical sulfide concentrations associated with the changes in chemocline depth. Using the isotopic composition of molybdenum in sediments as a proxy, we show for the first time that varying concentrations of dissolved sulfide can be fingerprinted in historical systems. Our molybdenum isotope data indicate that in the region of the Bosporus inlet, the chemocline rose more than 65 m, reaching concentrations over 100 μM sulfide in the bottom water ca. 300 yr B.P. This historical shoaling of the chemocline and extreme change in bottom-water sulfide concentration exceeds the modern changes that have been observed directly and attributed to anthropogenic influences on the Black Sea chemistry/hydrology. The first cold interval of the Little Ice Age, when temperature and circulation changes occurred in the Black Sea basins, may have provided the natural trigger for this extreme rise in bottom-water sulfide concentrations.