In this study, water quality and mud property in inner part of the Ariake Sea were examined through analyzing field survey data and laboratory tests for the basic parameters. As a result, state of anaerobic and/or reduction in summer season is found to be significant phenomena in deeper water in western part area of the Ariake Sea. Averaged particle size of mud in western part of the sea is mostly silt-clay with high organic content. It shows that the deposit mud can be resuspended quickly because the water content of the mud is very high (about w=300%). Also the mud property of high organic content gives some possibility of oxygen consumption in relating with resuspension and sedimentation of the mud. Water quality simulations were carried out to analyze mass balance and major phenomena in this area. From some sensitive analysis on simulation parameters, monthly change of COD concentration in the inner part is affected by mud property and rate of algae production although total loading through main rivers is not so significant except rainy season.