A yard submerged with flood water from the Limpopo river on 5 February 2026 in Xai Xai, Mozambique. Zinyange Auntony/Getty Images When floods sweep through southern Africa, the most visible damage is immediate: homes washed away, crops destroyed, clinics disrupted, families displaced. These images dominate headlines and humanitarian appeals.But as floodwaters recede, a quieter, slower-moving crisis often follows – in those same communities that are already struggling to recover. In parts of Mozambique, Malawi, Tanzania, Zambia, Zimbabwe and South Africa, severe rainfall and flooding in early 2026 reshaped daily life for hundreds of thousands of people. As communities clear debris and try to rebuild livelihoods, they are also entering the most dangerous window for malaria transmission.We are scientists from the University of Pretoria Institute for Sustainable Malaria Control. Our institute has the Remote Sensing for Malaria Control in Africa programme, which uses satellite data, remote sensing and environmental modelling to study malaria. It focuses on how climate variability and change influence transmission drivers like rainfall, temperature, surface water, land usage, cross-border movement, vector ecology and parasite patterns. As climate-driven floods become more frequent in southern Africa, they are not only washing away infrastructure. They are reshaping malaria risk in ways that entrench poverty and threaten fragile progress towards elimination. For people living on the margins, floods do not arrive as isolated events. They trigger cascading risks that intensify existing poverty, strain already fragile services and further restrict access to healthcare. Homes, livelihoods and local infrastructure are often the first to fail. This deepens vulnerability long after the waters recede.There is another less visible threat: an increased risk of malaria transmission, as standing water and disrupted control programmes create ideal conditions for the disease to spread.Floods don’t just destroy; they create disease landscapesFlooding alters the environment in ways that favour malaria transmission. Malaria is a life-threatening, preventable disease caused by Plasmodium parasites and transmitted through the bites of infected Anopheles mosquitoes. It remains a serious public health threat in sub-Saharan Africa. In 2024, there were an estimated 282 million malaria cases and 610,000 deaths globally. The WHO African Region bore a disproportionate burden – 95% of cases and deaths. Malaria is estimated to cost Africa around US$12 billion per year in lost GDP.In South Africa, flooding in low-lying river basin areas such as the Limpopo region occurs frequently due to intense rainfall and climate variability, disrupting livelihoods and increasing malaria transmission risk.Rivers overflow and water spreads across fields and settlements. Then stagnant pools are left behind when water levels drop. These shallow, sunlit collections of water are ideal breeding sites for Anopheles mosquitoes, the vectors that transmit malaria.This means malaria risk typically rises weeks after the floods, not during the dramatic emergency phase. By the time the malaria threat emerges then, media attention has moved on, relief efforts are winding down, and households are expected to cope on their own.For wealthier communities, this risk can often be managed through prevention, early diagnosis and effective treatment. For poorer households, it is a very different story.Poverty, flooding and malaria – a dangerous triangleResearch shows that the communities most exposed to flooding are also those facing the deepest and most persistent poverty. They often live in low-lying areas and rely on climate-sensitive livelihoods. They also have limited access to safe housing, clean water and functioning health facilities. Read more: Malaria: new map shows which areas will be at risk because of global warming When floods hit, incomes collapse and assets are lost. Food insecurity rises. Health services are disrupted just when they are most needed. In these conditions, malaria becomes far more than an infection; it becomes a poverty multiplier.A single malaria episode can mean days or weeks of lost work, transport costs to reach distant clinics, and out-of-pocket spending on care. For children and pregnant women, the consequences are even more severe, with malaria contributing to anaemia, poor pregnancy outcomes and preventable deaths. Read more: Heavy rains put Kenya at risk of mosquito-borne diseases Floods expose inequalities between rural and urban areas, between provinces, and between those with access to services and those without. Malaria entrenches them. However, flooding doesn’t only increase malaria risk biologically. It also weakens the systems meant to respond.Clinics may be damaged or inaccessible. Supply chains for medicines and diagnostic tests are interrupted. Health workers are stretched thin by emergency demands. For displaced families, continuity of care is easily lost.This creates a dangerous lag: malaria transmission intensifies just as the ability to detect and treat cases declines. By the time severe illness becomes visible, opportunities for early intervention have already been missed. Delays in diagnosis increase the risk of severe disease, particularly among children.Climate change is turning shocks into cyclesExtreme rainfall and flooding are no longer rare events. Climate change is increasing both their intensity and their regularity across the region. For poor communities, this means recovery periods are shrinking, while risks are stacking.Malaria control strategies that assume stable seasons and predictable transmission patterns are being tested. Areas previously considered low risk may experience outbreaks. The already uneven progress towards malaria elimination becomes fragile.Without adaptation, gains made over decades in the fight against malaria can be reversed in a matter of seasons.What needs to changeResponding to floods without factoring in malaria risk leaves communities exposed. Likewise, malaria strategies that ignore the realities of poverty, displacement and disrupted services will fall short.Effective responses need to operate on multiple fronts:early surveillance and preparedness in flood-prone areas rapid restoration of access to diagnosis and treatment clear, accessible community awareness, even in areas not considered endemicregional coordination, because malaria does not respect borders leadership capacity within malaria control programmes to manage and limit risk.National control programmes, local governments and community stakeholders should drive these initiatives together, supported by regional and international health agencies. Research and expertise are not enough. We need to build capacity in areas like medical entomology, parasite biology and global health leadership.Ultimately, reducing malaria risk in flood-affected communities requires sustained investment in health systems, infrastructure and social protection. These are the same foundations needed to break broader cycles of vulnerability.Southern Africa will face more frequent climate shocks. The question is not whether floods will return, but whether communities will face them better prepared, with stronger systems, and fewer threats waiting in the aftermath.Tiaan de Jager receives funding from Gates Foundation. Taneshka Kruger does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.