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In paleoceanography, physical and chemical processes of the oceans are studied throughout geological history. The sediments that constantly accumulate on the sea floor reflect the oceanographic conditions at the time of deposition. These geological records can be collected using sediment cores, providing a window into the past. In January 2016, sediment core 64PE406-E1 was collected in the eastern Mediterranean Sea, near Cyprus, which inspired the research presented in this thesis. The geological record of the Mediterranean sea contains alternating dark organic rich layers, so-called sapropels, and gray mud layers. We study the oceanographic mechanisms that cause sapropel formation in the Mediterranean Sea, as well as organic rich deposits in the Black Sea. The key to sapropel formation is water circulation and organic matter. When the circulation slows down and sufficient organic matter is produced, the bottom water becomes anoxic, i.e. lacking oxygen. Any organic matter that sinks to the sea floor is preserved, hence the dark colour. Due to the lack of oxygen, life does not disturb the sediments on the sea floor. Consequently, these sediments provide a remarkably fine structure of layers and a high resolution record of past oceanographic conditions. In the Mediterranean Sea, sapopels are found at a regular time interval of typically 21 thousand years, equal to the period of Earth's precession. Indeed, Earth's motion is an important drivers of climate change on geological timescales. In particular, Earth’s precession impacts the monsoon intensity, which in turn determines the Nile discharge. The Black Sea was cut-off from the Mediterranean during the last ice age, since the sea level was not high enough for water to pass the shallow Bosporus strait. At the end of the ice age, the sea level increased, allowing inflow from the Mediterranean Sea. The in-flowing water sank to the deep parts of the basin, supplying extra nutrients into the Black Sea. Consequently, production of organic matter increased, causing the formation of an organic rich layer. Previous studies often do not describe transient behaviour. In contrast, we present a transient box model that captures oceanic circulation. In such a model the basin divided in a small number of boxes, each representing an important water mass. They interact by exchanging salt, heat, oxygen and nutrients. The great advantage of this approach is that it gives insight into the fundamental processes. The model describe long term (> 100 kyr) processes on a one year resolution, while being computationally light. We conclude that sapropel formation in the Mediterranean Sea is an inherently transient process. In the Black Sea, a steady state is reached with a high organic carbon burial rate, resulting in a single organic rich deposit. A monotonic sea-level curve shows the best match with the geological data of the Black Sea. We find that our model describes the main trends found in geological records of both the Mediterranean Sea and Black Sea.