Graphene and its counterparts have been widely used for the removal of contaminants from (waste)water but with limited success for the removal of pharmaceutical contaminants. Driven by this need, this study reports, for the first time, the removal of pharmaceuticals from real contaminated water samples using porous graphene (PG) as a filter-based column. This work systematically evaluates the performance of PG as a filter medium for the removal of widely consumed pharmaceutical/emerging contaminants (ECs) such as atenolol, carbamazepine, ciprofloxacin, diclofenac, gemfibrozil and ibuprofen. Several factors were investigated in these column studies, including different reactive layer configurations, bed packing heights (5–45 mm), filter sizes (inner diameter 18–40 mm), adsorbent dosages (100–500 mg-PG) and water bodies (distilled water, greywater, and actual effluent wastewater). Sustainable synthesis of PG was carried out followed by its use as a filter medium for the removal of pharmaceuticals at high concentrations (10.5 ± 0.5 mg/L) and trace concentrations (1 mg/L). These findings revealed that the double-layered PG-sand column outperformed a PG single-layered configuration for the removal of most of the ECs. The removal efficiency of ECs from their solutions was improved by increasing PG dosages and filter bed height and size. Although the treatment of mixed pharmaceutical solutions from different water bodies was affected by the negative interference caused by competing water compounds, the treatment of ECs-contaminated greywater was not severely affected. Our findings suggest that PG, as a highly efficient filter medium, could be used for the removal of emerging pharmaceutical contaminants from water and wastewater.