The El Niño event in 2015/2016 was one of the strongest since at least 1950. Through surveys and interviews with key informants, we found businesses in the capital cities of Zambia, Botswana and Kenya experienced major disruption to their activities from El Niño related hydroelectric load shedding, water supply disruption and flooding, respectively. Yet, during the 2015/2016 El Niño, fluctuations in precipitation were not extreme considering the strength of the El Niño event. Results therefore highlight that even fairly moderate precipitation anomalies can contribute to major disruption to economic activity. Addressing the risk of disruption – and supporting the private sector to adapt – is a development priority.