Closely spaced samples of carbonaceous shales and siltstones from two upwards coarsening deltaic parasequences of the early Paleoproterozoic Timeball Hill Formation of the Pretoria Group, Transvaal Supergroup were analysed for their organic carbon content and isotopic composition. We illustrate that trends in the organic carbon isotopic signature are closely linked to changes in the depositional environment and also to variations in climate. Systematic trends displayed by organic carbon isotope values suggest that a biosynthetic chain transporting organic carbon from the oxygen-rich surface water to anoxic deep water was already present in the early Paleoproterozoic Ocean. Just as in modern deltaic environments, aerobic degradation of organic matter occurred in the shallow water and recycling of organic matter in the deeper water led to the preservation of isotopically light organic carbon. Sampling in a sequence stratigraphic framework also reveals that over time, the preserved organic matter became more13C enriched. This trend may be linked to a global decrease in atmospheric CO2 which eventually led to a major ice-age that is recorded by glacial diamictite capping the Timeball Hill Formation. The results confirm that in order to reach a better understanding of organic carbon cycling in the Precambrian, sedimentary facies, depositional environment and post-depositional modifications of carbon isotopic values must be taken into account.