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Sustainable land use planning involves both policy- and farmer-oriented agricultural land use strategies. In this paper, a spatially and temporally explicit multi-scale decision support system that reveals the biophysical indicators affecting land use choices of these different stakeholders, is explained and demonstrated. It comprises three different environmental assessment tools, designed to run with data supplied by traditional soil surveys and organised into a land resources information system. A qualitative land suitability classification procedure is adapted to translate the large-scale biophysical data supplied by a reconnaissance soil survey, into five suitability classes. At local scale, the productivity of the soil units identified during the semi-detailed soil survey is estimated using a three-level hierarchical crop productivity estimator, simulating the potential, water-limited and land production potential. At the smallest spatial and temporal resolution, a daily water balance approach is linked to a crop growth model, using daily climatic data recorded at different meteorological stations and the description, physical and chemical analyses of the soil profiles. The decision support system was applied and validated using the land resources information system of Rwanda. The system was capable to reveal the biophysical properties affecting crop regionalisation at national and local scale. Yield gaps between the potential, water-limited and land production potential, identified options for productivity optimisation such as irrigation or fertilisation. The crop growth model illustrated the delicate equilibrium between sowing date, crop cycle length and the length of the rainy seasons, limiting options for intensification. Combination of a multi-scale nature with scale-specific environmental assessment tools thus proved successful in identifying the different driving forces affecting land use choices made by different stakeholders involved, ranging from agricultural policy makers to individual farmers. This comprehensive approach is essential to realistic and sustainable land use planning.