Due to the pressure on South Africa’s irrigated agriculture to improve efficiency and optimal water use, irrigators must consider alternative water sources, such as root-accessible shallow groundwater tables, to supply the crop evapotranspiration requirement. Devising irrigation scheduling strategies that will optimize conjunctive water use is difficult because the contribution of shallow groundwater tables is not directly observed and is a function of irrigation management decisions; as a result, very few irrigators use these strategies. This paper aims to evaluate the profitability of using shallow groundwater tables as a source of irrigation water to satisfy crop evapotranspiration requirements. A bio-economic simulation model consisting of the soil–water–atmosphere–plant model and an economic accounting module was developed to calculate the profitability of conjunctive irrigation practices under different states of nature. The bio-economic simulation model was linked to a differential evolutionary algorithm to optimize the irrigation scheduling decisions. The results showed that irrigators could substantially increase profitability and water use efficiency if they consider the shallow groundwater table in their irrigation decision. About 51% of crop evapotranspiration could originate from shallow groundwater tables, reducing the irrigation requirements substantially without impacting crop yields. Sequential adaptive irrigation decision-making does not improve the bio-economic indicators much since using the shallow groundwater table mitigates the risk of undersupplying water. Therefore, conjunctive water use strategies using shallow groundwater tables economically benefit irrigators. However, a complex interplay exists between irrigation adjustments, crop yields and economic performance in different states, emphasizing the careful consideration of context-specific factors in irrigation management decisions.