Scanning electron microscopy of the scales of Cyprinus carpio, inhabiting two government-sponsored fish farms, with different sources of pollutants, in the North-East state of Meghalaya, India revealed extensive damage to them. Lepidonts, which are teeth-like structures present on the edge of circulii, were discovered to be either partly or completely damaged. The dislodgment of complete rows of lepidonts along with broken lepidonts was also observed. Loss of symmetry and torn areas of circulii are some of the abnormalities also observed as compared to control samples. The alterations observed could be because of the high sensitivity of the scales to environmental stress and their capacity to react to low concentrations of pollutants, which makes them a sensitive bioindicator of water pollution. The study hence not only represents an advance in pollution research, by employing a highly sophisticated analytical approach to reveal the above-mentioned microstructural scale abnormalities, but it can also have scientific impact on the society at large and the fish culturist in particular in understanding the destructive impact of pollution caused by mismanagement of city garbage and agricultural effluents.