Climate change is likely to affect the nature of pathogens/ chemicals in the environment and their fate and transport. We assess the implications of climate change for changes in human exposures to pathogens/chemicals in agricultural systems in the UK and discuss the effects on health impacts, using expert input and literature on climate change; health effects from exposure to pathogens/chemicals arising from agriculture; inputs of chemicals/pathogens to agricultural systems; and human exposure pathways for pathogens/chemicals in agricultural systems. We established the evidence base for health effects of chemicals/pathogens in the agricultural environment; determined the potential implications of climate change on chemical/pathogen inputs in agricultural systems; and explored the effects of climate change on environmental transport and fate of various contaminants. We merged data to assess the implications of climate change in terms of indirect human exposure to pathogens/chemicals in agricultural systems, and defined recommendations on future research and policy changes to manage adverse increases in risks.