Managing water and food systems in South Africa is complex given the factors involved in sustainably managing the sector. To ensure sustainable management of water and agricultural systems, equal access to natural resources, and economic equality, the government has implemented policies to regulate the systems and ensure economic growth. However, the unintended consequences of these policies on the sustainability of water and agricultural systems have not been fully understood in South Africa. This paper identified and analysed four system archetypes believed to have implications for current water and agricultural development policies in South Africa. These are ‘Limits to Growth’, ‘Fixes that Fail’, ‘Shifting the Burden’, and the ‘Attractiveness Principle’. The results show that policies implemented by the government ensure inclusiveness, equal access to natural resources, and improve productivity in the short‐term; the unintended consequences will ultimately undermine sustainability and food security over time.