South Africa has one of the highest child mortality and stunting rates in the world. Flexible geoadditive models were used to investigate the geospatial variations in child mortality and stunting in South Africa. We used consecutive rounds of national surveys (2008-2017). The child mortality declined from 31percent to 24percent over time. Lack of medical insurance, black ethnicity, low-socioeconomic conditions, and poor housing conditions were identified as the most significant correlates of child mortality. The model predicted degrees of freedom which was estimated as 19.55 (p<0.001), provided compelling evidence for sub-geographical level variations in child mortality which ranged from 6percent to 35percent across the country. Population level impact of the distal characteristics on child mortality and stunting exceeded that of other risk factors. Geospatial analysis can help in monitoring trends in child mortality over time and in evaluating the impact of health interventions.