In many riverine marginal wetlands water management is a main goal for nature conservation. However, sediments contaminated by organic chemicals and heavy metals often pose a potential risk for the ecosystem. The framework for our study is the wetlands of the rivers Weiße Elster and Parthe near Leipzig (Germany). We developed a conceptual model that links processes of sediment transport and biodegradation. The hydrological processes are described by a simplified advection-diffusion equation. The submodel for biodegradation includes a logistic equation and a Michaelis-Menten-like approach. It characterizes the growth of heterotrophic bacteria populations degrading contaminants. Hydrological parameters greatly affect the growth of the bacteria as well as the spatial distribution of accumulated contaminants. The spatial pattern of the metabolites differs significantly from that of the contaminants. As metabolites are also suspected to be toxic, they cannot be neglected. We discuss strategies to minimize negative impacts of contaminated sediments influencing the spatial arrangement of the overall risk potential.