The effectiveness of bank filtration (BF) is highly dependent on the source water quality (e.g., organic matter composition, pH, and concentration of heavy metals (HMs)). In this study, the impact of dissolved organic matter (DOM) on the removal of selected metals (Cu, Zn, Pb, Se, and Ni) during BF was investigated. Column studies were conducted at 30 °C with feed water sources of different organic matter composition. Excitation–emission matrix fluorescence coupled with parallel factor analysis (PARAFAC–EEM) was used to characterise the organic composition of the feed waters. Moreover, another series of column studies was conducted to assess the impact of natural organic matter type (humic, protein) and concentration on the HMs removals. The experimental results revealed a high Pb(II) removal efficiency during filtration, which depends only slightly on the organic matter content of the feed water. In comparison, the removals of Cu, Zn and Ni ranged between 65 and 95 %; and relied significantly on the organic concentration and composition in the raw waters. Humic compounds (terrestrial or microbial) demonstrated adequate ability to reduce the removal efficiencies of these HMs during the infiltration. Conversely, biodegradable matter was found to be effective in enhancing the sorption of HMs onto the sand grains. The Se-removal was enhanced when the feed water contained a higher concentration of biodegradable matter. In general, it can be concluded that the organic composition of the source water affects profoundly the removal of HMs during the BF, and should be considered in the design of BF systems.