El Niño has hit Africa particularly hard this year. The unpredictable weather cycle has been more intense than past iterations, and is being blamed for everything, from drought in southern Africa to excessive typhoons in Madagascar.

The humanitarian impact of El Niño is clear. The United Nations’ Children’s Fund (UNICEF) has warned that some 11-million children are at risk from hunger, disease and water shortages as a direct result of the extreme weather, with drought-stricken Ethiopia the worst affected. ‘The consequences could ripple through generations unless affected communities receive support,’ it said in a statement.

Aside from the obvious and devastating implications to the health and well-being of individuals, El Niño brings with it the possibility of dangerous economic and political instability - the kind that has unseated governments in the past.

South Africa is an interesting case study. As Africa’s most developed economy, and arguably its most successful democracy, South Africa should be more resistant than most other countries to political upheaval and popular discontent. But even here, the severity of the weather-induced crisis is raising unsettling questions for the government. With almost no rain this year, following on from a dry season last year, five of the country’s nine provinces have been declared disaster areas for agriculture.

South Africa, usually a net exporter of food, is having to import maize from South America, while thousands of farms may go out of business. The impact on small-scale subsistence farmers is even harsher, and the government has already announced a R220-million bailout package to limit the damage.The impact of this year’s near-total crop failure is being felt most in food markets, where prices are skyrocketing. According to Thabi Nkosi, senior economist for AgriSA, there has been a 14% increase in the cost of maize meal and a 7% increase in bread; both staples for South Africans. Eggs have risen by 15%, and chicken by 4%. More increases are expected. For now, beef remains relatively cheap, but only because desperate farmers – unable to feed or water their cattle – are selling off their stock. Once the market has absorbed the glut, the price of beef will increase dramatically.

It’s no wonder that Finance Minister Nhlanhla Nene is worried. ‘If it's long, indeed it will have serious impact on the food prices. It will have an impact on economic growth, because agriculture is one of our focus areas. It would also have an impact on employment; it would have an impact on our revenues. We are bracing ourselves for the worst,’ he said. But what, exactly, is the worst?

Louis Meintjes, president of the Transvaal Agricultural Union, has an idea. ‘When the maize crop goes down, the circumstances for social unrest go up. Then the unrest shifts from the farm community to the township and the offices of local government. Local officials have not been trained for this kind of situation and call in the police. The police have even been less trained and resort to strong-arm tactics: very soon government is fighting its own population. This is exactly how the Arab Spring in the Middle East started,’ he said.At first glance, this sounds like a stretch: how does one get from expensive groceries to a revolution? But the link is not as tenuous as one might think. Soaring food prices played a major role in precipitating the Egyptian revolution, and may have kick-started the Syrian war.

An article in Scientific American quotes Richard Seager, a climate scientist at Columbia University’s Lamont-Doherty Earth Observatory, as explaining: ‘Drying and drought in Syria from 2006 to 2011 – the worst on record there – destroyed agriculture, causing many farm families to migrate to cities. The influx added to social stresses already created by refugees pouring in from the war in Iraq.’ According to Seager, food prices increased, thereby aggravating poverty. ‘“We’re not saying the drought caused the war,” Seager said. “We’re saying that added to all the other stressors, it helped kick things over the threshold into open conflict. And a drought of that severity was made much more likely by the ongoing human-driven drying of that region.”’

Of course, conditions in South Africa are very different to those in Syria. Nonetheless, there is a very real risk that the drought will exacerbate underlying political tensions, especially on the touchy issue of land reform. According to AgriSA, the commercial farmers most likely to struggle financially as a result of the drought – the ones most likely to go out of business – are new black farmers who have taken up farming as part of South Africa’s land redistribution process. These farmers are unlikely to have the financial reserves necessary to tide them over until more prosperous times.The drought could set back the process of land reform by years, if not decades. This, coupled with rising food prices and growing unemployment predicted by the finance minister, could well spark a period of widespread political unrest.

If South Africa is nervous, other countries in Africa may have even more reason to fear. Ethiopia, for example, could be in real trouble. Its autocratic government justifies the suppression of civil rights by pointing to impressive economic growth and poverty alleviation strategies that are working. But what if the economy stops growing? What if people start sliding back into poverty as a result of the drought? Like in Egypt, where Hosni Mubarak’s regime only came under serious pressure once he stopped holding up his side of the social contract, Ethiopians may become intolerant of an autocratic government if the cost of living rises too dramatically.

At the moment, it is mostly farmers, meteorologists and humanitarian agencies raising the alarm about the extreme weather that El Niño is bringing to Africa. As the weather worsens, it’s worth remembering that these kinds of events have the potential to destroy more than just crops.

Written by Simon Allison, ISS Consultant