Subsistence farmers in Africa are often dependent on food grown within a limited area. Therefore, their health is often associated with geochemical factors that influence the soil-to-crop transfer of essential micronutrients (MN) for health (e.g. zinc). Food production and quality is compromised by soil erosion and downstream transport of sediments to waterbodies where sediment and associated nutrients/pollutants impact water security. Resources to manage soils sustainably can be limited, resulting in weathering and erosion of soil into waterways/catchments, such as Lake Victoria. Little is known about the loss of MN from weathering of soils and whether these are more prone to poor soil management (organic retention). Loss of fine soil particles may result in transfer of micronutrients or naturally occurring/anthropogenic potentially harmful elements (PHEs) into water courses/catchments with implications for ecological health. The Winam Gulf catchment of Lake Victoria is an exemplar of these processes as a regionally important source of food both from land and water.