This study aims to determine the water quality of the Mako-mako river based on physical, chemical and microorganism parameters as well as the effect of metal and microorganism levels on the color of the water and sediment of the Mako-mako river. The method of sampling water, sediment and plankton by purposive sampling at three locations, namely the upstream, middle and downstream of the river. The concentrations of Fe and Mn in water and sediment were analyzed using AAS, while the identification of plankton using a binocular microscope. The results of the analysis of the water quality of the Mako-mako river show that the parameters of temperature, TDS, TSS and Mn are still below the water quality standard for class 1, except for the Fe and total coliform parameters whose concentrations have exceeded the water quality standard. The metal content of Fe in sediment is high and affects the color of the Mako-mako river sediment which is reddish brown to dark brown (deep). The presence of plankton with a low level of abundance and diversity index did not affect the color of the river water or the sediment of the Mako-mako riverSo that to use the Mako-mako river water as a source of raw water, clean water needs to go through a processing process.