The role of in-stream aquatic vegetation as ecosystem engineers in the distribution of organic matter was investigated in the Okavango Delta, one of the world’s largest oligotrophic wetlands. The Okavango channel beds are covered up to 50% with submerged macrophyte patches. By accumulating and concentrating organic matter in the sediments below the patches, macrophytes are likely able to locally forestall a deficiency of nutrients. Up to 21 times more N, 18 times more C, 13 times more P and 6 times more Si can be found in vegetated sediments compared to non-vegetated sediments. Nutrient specific accumulation relates to its relative scarcity in the overlaying water. There is a depletion of dissolved N relative to P, whereas Si is relatively abundant. The Okavango Delta water can generally be characterised as oligotrophic based on plant species composition (e.g. presence of carnivorous plants and absence of floating plants), low plant N:P ratios, and low nutrient- and element-concentrations. Local mineralization and intensified nutrient cycling in the sediments is hypothesized to be crucial for the macrophytes’ survival because it provides a key source of the essential nutrients which plants otherwise cannot obtain in sufficient quantities from the nutrient poor water. By engineering the ecosystem as such, channel vegetation also retards the loss of elements and nutrients to island groundwater flow, contributing to one of the key processes driving the high productivity of the Okavango Delta, making it unique among its kind.