Water pollution is gradually increasing in natural waters through anthropogenic activities. This study aimed to use fish scales as a bio-indicator of pollution, along with water quality parameters, and the assessment and detection of selected heavy metals in water samples collected from the River Chenab, including the Chakbandi drain that gathers domestic sewage waste and industrial effluents from Faisalabad and deposits it into this freshwater body. All water quality parameters (pH, total dissolved solids (TDS), total suspended solids (TSS), salinity, conductivity, biochemical oxygen demand (BOD), chemical oxygen demand (COD), phenols and sulphates) and concentrations of selected heavy metals (Cd, Cu, Mn, Pb and Cr) were found to be considerably higher than permissible limits as defined by the WHO, and therefore capable of causing ill health effects in aquatic organisms. Specimens of fish scales from selected fish were described qualitatively and observed quantitatively. In Catla catla, Labeo rohita and Cirrhinus mrigala, the scales showed several deformities in shape and different scale structures such as circuli, radii and annuli. In each of the three types of fish, considerable variation in the morphology of their scales was observed in specimens collected from polluted sites.