Several types of pollutants have acute adverse effects on living bodies, and the effective removal of these pollutants remains a challenge. Safranin O (a biological dye) and merbromin (a topical mercury-containing antiseptic) are considered organic pollutants, and there are only a few reports on their removal. Synthesized and well-characterized (through PXRD, FTIR, FESEM, and EDS analysis) MOF-5 was used for the first time in the removal of safranin O and merbromin from simulated wastewater and real wastewater. In both cases, MOF-5 effectively removed contaminants. We found that in simulated wastewater, the highest efficiency of removal of safranin O was 53.27% (for 15 mg/L) at pH 10, and for merbromin, it was 41.49% (for 25 mg/L) at pH 6. In the case of real wastewater containing natural ions (Na+, K+, F−, Cl−, SO42−, PO43−, Mg2+, and Ca2+) and other molecules, the removal efficiencies of these two dyes decreased (34.00% and 26.28% for safranin O and merbromin, respectively) because of the presence of other ions and molecules. A plausible mechanism for the removal of these pollutants using MOF-5 was proposed.