<p>Waterborne diseases are caused by pathogens that are transmitted via ingestion of contaminated water and remain a leading cause of death particularly in young children. Climate change threatens to undermine the progress that has been made in reducing waterborne diseases. In this Review, we explore how meteorological conditions that are influenced by climate change, including temperature, heavy rainfall and flooding, drought, and extreme weather, affect the biology and transmission of waterborne pathogens, with a focus on those that spread via the faecal–oral route. We discuss evidence that these impacts vary across pathogens and consider how such information is used to project disease risks under future climatic conditions, including incorporating social vulnerability and pathogen-specific outcomes to more accurately estimate future disease burden. We also review strategies to blunt climate-related increases in waterborne diseases, including vaccination; water, sanitation and hygiene interventions; and enhanced surveillance. As climate change continues to alter our global environment, understanding its impacts on waterborne diseases can improve our ability to reduce climate harms, identify and protect vulnerable populations, and develop evidence-based approaches to promote population health.</p>