The main aim of the study was to develop the method determining adsorption capacity, regeneration ability and aggregation tendency of metal-doped carbon-silica composites (iron-doped, C/Fe/SiO2 and manganese-doped, C/Mn/SiO2) against heavy metals and selected organic substances. The properties of these composites were compared with those of metal-free silica-carbon composite (C/SiO2). Inductively coupled plasma-optical emission spectrometry (ICP OES) and high-pressure liquid chromatography (HPLC) were used to determine adsorbed amounts and desorption degree of organic/inorganic pollutants. Potentiometric titrations and electrophoretic mobility measurements were conducted to understand the mechanisms driving adsorption and particle aggregation. The size of aggregates formed in the systems as well as the stability of the examined suspension were estimated using UV-VIS spectrophotometry. The performed experiments showed that the selected combination of methods is appropriate to determine potential of metal-doped carbon-silica composites as adsorbents as well as the ease of their removal with adsorbed contaminants from aqueous solutions by sedimentation.