Pharmaceutical compounds are designed to elicit a biological reaction in specific organisms. However, they may also elicit a biological response in non-specific organisms when exposed to ambient quantities. Therefore, the potential human health hazards and environmental effects associated with pharmaceutically active compounds presented in aquatic environments are being studied by researchers all over the world. Owing to their broad-spectrum occurrence in various environmental matrices, direct or indirect environmental hazardous impacts, and human-health related consequences, several pharmaceutically active compounds have been categorized as emerging contaminants (ECs) of top concern. ECs are often recalcitrant and resistant to abate from water matrices. In this review, we have examined the classification, occurrence, and environmental hazards of pharmaceutically active compounds. Moreover, because of their toxicity and the inefficiency of wastewater treatment plants to remove pharmaceutical pollutants, novel wastewater remediation technologies are urgently required. Thus, we have also analyzed the recent advances in microbes-assisted bioremediation as a suitable, cost-effective, and eco-friendly alternative for the decontamination of pharmaceutical pollutants. Finally, the most important factors to reach optimal bioremediation are discussed.