<p>Soil carries out a diverse range of functions and provides critical services, without which human life would not be possible. The links between soil and water are intimate but insufficiently recognized. To understand how soil health underpins water quality, an integrated approach is needed that accounts for novel practices and emerging classes of micropollutants to minimize potential impacts on soil health, and ultimately water quality. This Review first sets the context and presents examples of micropollutant sources to soil, with a focus on resource reuse. We then discuss the dual roles of soil—as a potential source of contamination and as a filter that protects water resources from contamination—considering both relatively well-understood scenarios (for example, the application of pesticides) and emerging chemical threats (for example, pharmaceuticals and plastics). We conclude with recommendations linked to future policy and research agendas to adopt a truly ‘One Environment approach to One Health’ that fully recognizes the connections between environmental compartments including soil and water quality.</p>