Since the adoption of the Renewable Energy Sources Act in Germany in 2000 and its amendment in 2004, there is a well defined trend for the installation of biogas plants, and by extent a boost in crop cultivation for substrate provision. Currently, corn grown in monoculture or in tight crop rotations is the dominating crop for biogas production. The diversification and intensification of energy crop rotations by using autumn-sown catch crops, forage grasses, or whole crop small grains is intensively discussed at present. If water supply is not limiting growth, intensive energy crop rotations may allow for higher yields compared to maize monoculture, as recently demonstrated under environmental conditions of Southern Germany for crop rotations comprising winter rye or turnip rape followed by corn. In many regions of Germany, however, the use of highly productive crop rotations is restricted because of low water availability. The province of Schleswig-Holstein, located in Northern Germany, is characterized by relatively favourable rainfall supply, with annual precipitation ranging between 700 and 850 mm. In the joint research project BIOGAS-EXPERT the nitrogen and carbon flows as well as potential losses by leaching and volatilisation are quantified for defined energy crop rotations on two sites under the environmental conditions of Schleswig-Holstein in a first step, and modelled in a second step. The objective of the present study was to analyze the impact of crop rotation design on the soil moisture regime. To this end, the impact of environmental conditions (climate, soil) and crop rotation (corn monoculture, permanent grassland, and a corn-whole crop wheat-Italian ryegrass) on selected water balance parameters was quantified by a long-term (30-years) scenario simulation. The simulations were performed using the class-oriented programming environment HUME, corresponding modules for calculating the water balance together with the mechanistic crop growth model FOPROQ.