The accumulation of heavy metals in different areas is an indicator of toxicity. In this investigation, three fish species; namely,  Scarus pulchellus, Acanthopagrus bifasciatus, and Mugil cephalus were collected from different regions in Saudi Arabia (Jeddah, Tabuk and Al-Jubail).  Fish diversity, environmental parameters and scale structure were addressed. For the environmental parameters, some heavy metals (Zn, Mn, Cd and Cu) were estimated in water samples collected from the studied areas. The light microscopic structure of fish scale illustrated the shape of scale and malformations, giving each species its characteristic taxonomical order. The scales showed several deformities in shape and different scale structures such as circuli, radii and focus. With respect to the three fish species, a considerable variation in the morphology of their scales was observed in specimens collected from different sites. Finally, this study revealed important results showing the scale abnormalities as an important indicator that differed with the heavy metal concentrations in different regions. The result recommends setting a decision to prevent industrial and other pollution which led to harmful changes in the tested fishes and subsequently can cause serious effects on human health.