The sediment or fauna incubation experiment (SOFIE) is an experimental research tool that was developed to analyze concentrations and chemical speciation of heavy metals in pore waters of natural, undisturbed sediments or water-sediment interfaces over time, while simultaneously conducting exposure tests with sediment-dwelling organisms. In this way, concentrations of chemical species are directly linked to accumulation by biota. It is shown that discrete gradients of redox-sensitive metals and nutrients occur over very small intervals. These gradients differ from those of free metal ion activities. Speciation affects the uptake of metals by sediment-dwelling organisms, which, in their turn, have a significant effect on metal speciation. With reaction kinetics that differ per metal, uptake of metals by organisms from the water phase may be hindered (e.g., Cu, Zn) or promoted (e.g., Ni, As). Time-varying exposure concentrations of metals were incorporated in uptake and elimination models. Body concentrations of Cd, Cu, Ni, and Zn in the aquatic oligochaete Limnodrilus could best be described by the time-varying free ion concentration in the overlying water. Body concentrations of As and Pb were best described by sediment pore water concentrations. It is concluded that SOFIE provides the necessary experimental tool to support, in a mechanistic way, environmental risk assessments of contaminants.