Climate change will bring higher temperatures to Southern Africa while changing rainfall patterns will affect the amount of water available for food production.
"Irrigation is often listed as an adaptation strategy for farmers, but no one has really looked at the impact of climate change on irrigation," said Claudia Ringler, a Senior Research Fellow at the US-based International Food Policy Research Institute (IFPRI).
Ringler and her colleague, Tingju Zhu, a senior scientist at IFPRI's Environment and Production Technology Division, have published a series of research papers on the effect of various scenarios - from a business-as-usual approach where greenhouse gas emissions continue, to having environment-friendly policies in place - on water sources available for irrigation, such as rivers, groundwater and rainwater runoff, in various parts of Africa.
To measure this they took into account the rate of evapo-transpiration - the release of water into the atmosphere from surfaces such as soil and plants -and changes in rainfall.
One of their papers looked at the Limpopo River Basin, which crosses four Southern African countries - Botswana, South Africa, Zimbabwe and Mozambique - and provides a living to hundreds of thousands of farmers, and found that water supply would start diminishing in another two decades.
Nearly a quarter of South Africa's population of 48 million and 60 percent of Botswana's people live in the basin, which has 2.9 million hectares of farmland, with 91 percent cropped under rain-fed conditions. According to the Agricultural Research Council (ARC) of South Africa, half the basin's water is consumed by big commercial farms in South Africa and Zimbabwe.
Climate change will affect rainfall in the basin severely - it will receive between 10 and 25 percent less in the next two decades - so more and more farmers will turn to irrigation, the IFPRI scientists said.
At present the water in the Limpopo River basin supplies the irrigation needs of 97 farmers out of every 100 in every second year; in another two decades this number will drop to 91 out of every 100 farmers, Ringler said.
Rainfall in the basin is highly seasonal and unevenly distributed, already affecting food production in the region, and climate change projections indicate that floods and droughts will worsen.
Commercial farmers make up 20 percent of the farming population in the basin and own 60 percent of the land, while the remaining 80 percent are small-scale farmers with 20 percent of the land, and therein lies the problem.
"The commercial farmers ... are well prepared for the water-stressed scenario with drip irrigation systems in place and access to drought-tolerant seed varieties," said Ringler. Most of the small-scale farmers also depend on the river for irrigation but do not have access to drip irrigation systems, which use very little water.
The farmers also face stiff competition for water from the gold, platinum, coal and iron mines in South Africa's share of the basin, and half of South Africa's electricity is generated by the coal-fired plants located in the basin, according to ARC.
Most of the basin - 45 percent - falls within South Africa's borders and its needs dictate the share of water that other countries in the region receive, Ringler said. The escalating climate-related stresses and existing competition for water mean the potential to expand irrigation is limited.
"All the countries will have to work together to create an equal playing field in sharing the water," she pointed out. "South Africa could create a water reserve for the Mozambican farmers who live downstream."