This study describes the ocean circulation of the Indonesian Seas based on results using a 3D regional model. The study is divided into 3 parts. In the first part, Chapter 2, the basic properties of a developed regional model of the circulation of the Indonesian Seas are outlined. It is well known that the complex topography of the region strongly influences temperature, salinity and current distributions there. The main objective of the second part, Chapter 3, is to analyze the basic features of potential temperature and salinity distributions in the Indonesian Seas simulated by the model. The influence of bottom topography on the formation of temperature and salinity distributions is considered by following the three major routes of flow of North Pacific and South Pacific Water through the Indonesian Seas. In the last part, Chapter 4, aspects of turbulence and mixing in the Indonesian Seas are presented and discussed.