Topsoils are often contaminated by trace metals, and it is important to understand how different processes govern the transport of such metals to fresh and marine waters. This paper presents measurements of natural nanoparticles and colloidal organic matter in soil and river samples from Germany and Sweden. In our analytical approach, a nanoparticle separation technique is combined with multielement detection and applied to soil and river samples to link the macroscale field observations with detailed molecular studies in the laboratory. It was determined that lead is associated with iron oxide colloids, which are ubiquitous nanoparticles that can be efficiently transported. Eventually both iron oxides and lead are removed by flocculation under conditions of estuarine mixing. Iron-rich nanoparticles compete efficiently with natural organic matter (NOM) complexation for lead binding in both the soil and river systems studied.