Livestock integrated land use systems are considered as viable options for enhancing soil organic carbon (SOC) sequestration in a changing climate. This study assessed the influence of water deficit and livestock stocking density on soil carbon stocks. A total of 101 matching data were extracted from map layers of water deficit and livestock stocking density for C storage in Arenosols of Omusati and Otjozondjupa regions of Namibia. Maps for water deficit and livestock stocking density were obtained from national databases. The SOC data were arranged into four treatment combinations represented by two levels of water deficit and two levels of livestock stocking density. Linear mixed models (LMM) were then used to evaluate differences in SOC stocks in response to livestock stocking density and water deficit. Results showed that there was a significant interaction (p = 0.013) between the effects of livestock stocking density and water deficit on C-stocks. In conditions where the water deficit was small, the SOC stock was larger under more intensive grazing. Whilst in conditions where water deficit was large, the SOC stock was larger under less intensive grazing. Furthermore, the difference between SOC stock at large and small water deficits was larger under more intensive grazing. This shows that the impacts of a changing climate, and changes in the intensity of grazing must be considered together to predict effects on the SOC stock.