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Subsistence agriculture systems in semi-arid regions need to adapt management to rainfall variability within the constraints of low-cost alternatives. Organic fertilization is generally the best possible option to maintain soil fertility as the use of chemical fertilizers is unfeasible due to the high cost and risks of drought and crop failure. However, the effectiveness of organic fertilization will vary according to the quality and rate of organic fertilizer application, rainfall scenarios and decomposition patterns. Simulation models can be used for a quick evaluation of management strategies in many possible scenarios. In this paper a newly developed model (SALSA: Semi-Arid Latin-america Simulation model for Agroecosystems), was used to simulate, along a 3-year period, plant productivity and soil fertility in a maize/native pasture rotation system in semi-arid NE Brazil. The model simulated reasonably well the observed maize productivity in the experimental plots during the 3 years of the study, even under contrasting rainfall conditions and application of organic fertilizers of different qualities (animal manure or Gliricidia sepium prunings). However, model simulations of native pasture biomass productivity did not adequately represent seasonal and fertilizer responses, in part probably due to the seasonal variability of the pasture species composition. The model showed that the effectiveness of organic fertilization depended upon rainfall with largest response in years with intermediate precipitation, and lower responses in wet and dry years. High nitrogen leaching and cloudiness reduced fertilizer use efficiency in wet years even at high rates of fertilizer application (20 t ha(-1)). Fertilization with G. sepium did not increase aboveground maize productivity compared with animal manure, even though it contained twice the amount of labile fraction. This lack of crop responses to a more labile fertilizer is explained by the large fraction of nitrogen that is leached to deep soil which reduced nitrogen availability in the volume of the soil with the largest amount of crop roots. Management strategies that reduce nitrogen leaching or favor pumping nitrogen from deeper layers (agroforestry) would benefit productivity in this system. The SALSA model proved to have potential as a useful tool to help decisions needed to increase organic fertilization efficiency in NE Brazil even though the base information is scarce compared with modern agriculture. (c) 2008 Elsevier B.V. All rights reserved.