Abstract Food production comes at an ecological cost, and the lack of sustainability of South Africa’s crop production systems is becoming increasingly worrisome. While small scale emerging and homestead subsistence farming are significant in the agricultural sector, food production is dominated by large scale commercial agriculture. In this paper we analyse the ecological impact of South African commercial crop production and what can be done about it. Impact categories considered are divided into what we consider ‘better-researched’ problems: fresh water depletion, salinisation, soil degradation, eutrophication and land use change; and into what we consider ‘emerging’ problems for agriculture: greenhouse gas emissions, soil profile acidification, ecotoxicity and non-renewable resource consumption. While there is a paucity of quantitative information, it is clear that after decades of cultivation many of our agroecosystems are degraded or degrading. Sustainable crop production and food security are ‘wicked’ problems – containing dynamic social, economic and biophysical complexities. Increased stakeholder engagement to better understand these problems, the tradeoffs linked to finding solutions and to involve those with the resources to turn knowledge into action is required. Collecting key data, turning it into information within local contexts (involving the ecology, agronomy, sociology, psychology, economics and other disciplines simultaneously) and communicating it effectively to allow learning and adaptive management at various spatial and temporal scales is essential. An example is the display of river flows on a website in real-time to help farmers manage and adapt irrigation practices better, and to connect them with other stakeholders to improve understanding of the responsibilities of managing water at local and catchment scales.