In order to assess the water quality of the Brantas River and the adjacent coastal areas of Java, Indonesia, an automated monitoring station has been developed and assembled inside a container at the banks of the river. Time series over a year show the seasonal (dry/wet) variations with dramatic bad water quality during dry season. From the day-night variations some estimations about biogeochemical processes can be derived. In order to assess the distribution of freshwater and related conservative water constituents a hydrodynamic 3D-model has been applied. The results show a high influence of the coastal waters during wet season but only local influences in front of the rivers during dry season.