The study on the photocatalytic activity of organic aerogels produced from Estonian oil shale processing by-products and doped with Fe, Ni, Cu, Zn and Co was performed for the first time in water treatment processes. The synthesis of aerogels from oil shale phenolic compounds is unique and promising approach in application of novel materials with photocatalytic properties. 2,6-Dihydroxy-4-methylbenzoic acid (dHMBA) with the ion-exchange moiety (carboxylic group) susceptible for the metal-doping and 5-methylresorcinol (MR) were selected for the synthesis of aerogels. Although these chemicals are commercially available, it was less costly and environmentally friendlier to use by-products from Estonian oil shale industry, which otherwise could be considered as production wastes. The bacteriostatic antibiotic trimethoprim (TMP) was selected as a target pollutant due to its environmental concern. TMP was found to be resistant to photolytic degradation and required the additional degradation improvement by means of photocatalysis. The unique structural features of studied materials allowed achieving the synergistic effect of adsorption and photocatalytic oxidation. The subjected hypothesis on the photocatalytic activity of studied metal-doped organic aerogels (Me[OA]s) except Cu[OA] was successfully confirmed, whereas the results of using Cu[OA] indicated the presence of combined photolysis and adsorption. Trimethoprim degradation followed oxygenation and demethylation pathways.