The water quality of Myntdu River at Jaintia Hills District Jowai has been studied as a comparative analysis of toxic metal seasonally during spring, monsoon, autumn and winter. The results showed the maximum metal content was obtains from the tributaries as compared from the originate source of Myntdu River in which value exceeded the permissible limit according to WHO (2006). The quality of river has deteriorated year by year due to the continuous discharge of domestic waste and coalmine seepage from various drains to the tributaries of Myntdu River. Therefore the water supply for domestic purposes from the Myntdu River should be treated and immediate action should be taken in order to stop the pollution load into the river water.