Pharmaceutical chemicals represent one of the major contaminants in the aquatic environment. Several studies have revealed their negative effects on non-target organisms. Pharmaceutical chemicals are constantly released into the environments and their chronic exposure at lower concentrations may impose a threat to the aquatic environment and human health. Pharmaceuticals have been reported in surface water as well as in groundwater which is the ultimate source of drinking water. Mostly antibiotics, anti-depressant, β-blocker, synthetic hormones, non-steroidal anti-inflammatory drugs, and analgesics have been detected in aquatic environments. Major sources of pharmaceuticals in the aquatic environment are sewage and WWTPs effluents, hospital discharge, and the effluents of pharmaceutical industries. Pharmaceuticals and their metabolites have been detected in fishes collected from different aquatic environments. Pharmaceutical chemicals disrupt the thyroid, reproductive, and neuroendocrine systems of fishes. The present study reviews the concentrations of pharmaceuticals in the aquatic environment and bioaccumulation in the fish body, and their toxicological impacts on the endocrine system to identify the knowledge gaps. This study suggests more extensive case studies for controlling pharmaceutical release into the environment and evaluating the ecological risks of emerging EDCs.