This case study is specifically aimed at testing the applicability limits in the near-shore areas of the open ocean equations upon which the OF-Mod 3D used in this study is based. The study was carried out using surface sediments from the Benguela upwelling system. Rock-Eval data used in this study was obtained from unpublished studies on surface sediments and suspended particulate matter carried out in the area along multiple transects (University of Berlin, DSDP Project). Marine primary productivity values ranging 70 – 370 (gC/m2yr) were used in three different productivity scenarios to simulate organic carbon (OC) deposition in the Benguela upwelling area. Two sets of equations (Mann, 2008)and(Müller and Suess, 1979) were used separately to generate results which were then compared with the measured results. The results show under the high productivity scenario that the two equations have different OC distribution on the shelf is generally < 2 percent for both equations except around the Walvis cell. OC distribution on the upper and lower slope for (Mann, 2008) averages around 3.5 percent (wt) and < 2 percent (wt) respectively, whereas OC distribution for (Müller and Suess, 1979) equations on the upper and lower slope averages 6 and 4 percent (wt) respectively. This indicates a general underestimation of OC. The software performance at water depths <100m was not so good. At water >100m, there were many intervals where the software works very well (difference of ≤ 20 percent between measured and modelled values) and at some intervals not so well (>20 percent).