A study was conducted to visualize the speciation of heavy metals—copper (Cu) and nickel (Ni)—in contaminated bottom sediments and their influence on the cleaning process using vibrating screens. It was shown that the metals in the studied samples were primarily present in the form of sulfides: either with dense cementation by clay material along the entire contour of the aggregate, or with localized (point) cementation by clay particles. A dense cementation effect of Cu and Ni aggregates along the contours on the surfaces of quartz and potassium feldspar grains was observed in samples with elevated organic matter content. It was found that low organic matter content resulted only in localized cementation of heavy metals. The average size of all observed nickel and copper sulfides did not exceed 10–15 μm. It was concluded that increasing the mesh size of the screen leads to a rise not only in the amount of heavy metals retained but also in the volume of soil passing through the screen. This may pose challenges due to the large-scale removal of the undersized ("clean") soil fraction, resulting in high transport and disposal costs.