Several areas around Kelantan River such as Gua Musang and Tanah Merah have been expected as polluted area due to the mining activities and oil palm industries located near to the river. However, there are still lack of evidence to support this theory. Therefore, this study has been carried out to determine the status of water quality at Lebir River (Gua Musang), Kenerong River (Dabong) and Estuary at Kelantan River (Tanah Merah) by determination of physical parameter and chemical parameter namely aluminium, lead, iron, cadmium, and zinc. In addition, the concentration of heavy metals in different species of fish muscles from Lebir River (Gua Musang), Kenerong River (Dabong) and Estuary at Kelantan River (Tanah Merah) were also investigated to assess the pollution level. The results showed the concentration of Al and Fe in river water at Tanah Merah were exceeds the World Health Organization (WHO). In addition, heavy metals in fish detected from the area of Tanah Merah shows the highest concentration compared to other areas. As conclusion, Kelantan River at Tanah Merah can be classified as the polluted area based on the heavy metals contents in the river water and fish muscles. These results can be used by Department of Environment (DOE) to monitor the pollution level in Kelantan River.