A model system has been generated for the buttom and water quality development of reservoirs during the first few decades of impounding. The model is based on 3D (three-dimensional: longitude × latitude × depth) calculation of the water currents, their variation with time and on 3D description of release, transport, degradation, settling and other processes affecting water quality and the bottom. Special attention in the model development has been paid to the effects of varying water levels and to the internal loading from the bottom. The latter is a combined result of several processes, including degradation of the former terrestial vegetation and organic matter in general, gas development and convective flows, and erosion caused by waves, currents and ice cover. Results from the Porttipahta Reservoir in Finnish Lappland are presented and compared with the field observations as an example of the model applications.