This study quantifies the potential effects of a set of technologies to address water and fertility constraints in rain-fed smallholder agriculture in South Africa, namely in situ water harvesting (WH), external WH, and ecological sanitation (Ecosan, fertilization with human urine). We used the Soil and Water Assessment Tool to model spatiotemporally differentiated effects on maize yield, river flow, evaporation, and transpiration. Ecosan met some of the plant nitrogen demands, which significantly increased maize yields by 12% and transpiration by 2% on average across South Africa. In situ and external WH did not significantly affect the yield, transpiration or river flow on the South Africa scale. However, external WH more than doubled the yields for specific seasons and locations. WH particularly increased the lowest yields. Significant water and nutrient demands remained even with WH and Ecosan management. Additional fertility enhancements raised the yield levels but also the yield variability, whereas soil moisture enhancements improved the yield stability. Hence, coupled policies addressing both constraints will likely be most effective for improving food security.