The model MACH3 calculates prognostically the three-dimensional distribution of temperature and salinity, and thus the temporal evolution of thermal and haline pycnoclines. Also, MACH3 is able to calculate the spreading of nutrients and the temporal and spatial evolution of the oxygen saturation in the water dependent on any oxygen depleting biochemical activity. Particularly for ecological investigations, the exact determination of these parameters is of great importance. Ecological problem zones like areas of potential oxygen deficiencies and over-fertilized areas can be detected, and the measures for improving the ecological conditions can be assessed and can be optimized. With the help of MACH3, the spreading and transport of plankton and fish larvae can be calculated including growth and mortality rate depending on the actual values of temperature and salinity. Thus, not only the route of a population can be determined but also its increase or decrease caused by changing water characteristics during the transport. Also, ecological effects of any planned river restoration with respect to establishing new biotopes dependent on current velocities, water exchange, nutrient transport, and ventilating can be assessed very well with MACH3.