A good water quality is significant to sustain the life of the organisms. The determination of water quality is needed as a direction to monitoring the water pollution. This purpose of this study is to examine the quality of the water and to determine the water pollution index based on physical-chemical 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 physical-chemical parameters of the waters are still appropriate to the biota marine in all study stations such as water turbidity, BOD, NH3 and heavy metals (Hg, As, Cd, Pb, Cu, Zn, Ni and Cr). However, there is parameter which the quality standards had been exceed in all locations such as water salinity for coral and seagrass, NO3, PO4 and H2S. The result of pollution index calculation at coastal waters Mimika are classified as lightly polluted (Keakwa and Pomako waters), medium polluted (Moga, Puriri, Inaoga and Atuka waters) with pollution index values of 3.51 to 6.95. This study is becoming important to notice that the parameters of quality standards which had been exceed such as NO3, PO4 and H2S are an environmental parameter for nutrient elements and can be a trigger for eutrophication in the waters