A good water quality is essential to sustaining the life of the organisms. The determination of water quality is needed as a direction to monitoring the water pollution. The purpose of this study is to examine the quality of the water and to determine the water pollution index based on the physicochemical parameters in Mimika waters, Indonesia. The sampling of water quality was carried out in October 2016 at six stations (Moga, Puriri, Inaoga, Keakwa, Atuka and Pomako waters). Then, the results were compared with the standard of sea water quality for biota marine based on the Decree of the Minister of Environment No. 51 year 2004. This study showed that the physicochemical parameters of the waters, such as water turbidity, BOD, NH 3 and heavy metals (Hg, As, Cd, Pb, Cu, Zn, Ni and Cr), are still appropriate to the biota marine in all study stations. However, there is a parameter for which the quality standards were exceed in all locations, including water salinity for coral and seagrass, NO 3 , PO 4 and H 2 S. The result of pollution index calculation at coastal waters Mimika are classified as lightly polluted (Keakwa and Pomako waters), and moderately polluted (Moga, Puriri, Inaoga and Atuka waters) with the pollution index values of 3.51 to 6.95. It is important to notice that the parameters of quality standards which had been exceed such as NO 3 , PO 4 and H 2 S are the environmental parameter for nutrient elements and can trigger eutrophication in the waters.