A wide variety of computer-based models and tools have been developed to describe and characterize agricultural production systems. For complex problems, however, no single application is available nor is it advisable to develop one for practical reasons. Integration of models and tools may be a solution, where limitations of some may be compensated for by others. Different models and tools were integrated for the analysis of different land-use scenarios for the Neguev settlement in the perhumid tropical low-lands of Costa Rica. Crop-growth simulation models and expert systems were used for the description of alternative land-use systems. A geographical information system was used for data storage, and the analysis and presentation of results. The optimization of land-use was carried out by a linear programming model. Using a series of relevant land-use scenarios, effects are studied of: (i) changes in capital availability; (ii) restrictions on biocide use; and (iii) the effect of nutrient depletion as a negative contribution to farm income. For the integration of models and tools, a modular approach is proposed, which is based on separate software packages and appropriate database structures. The database structures can be jointly used by the different modules and form the link between them. In addition, a separate software package is used for the integration of the modules. The methodology is particularly appropriate for interdisciplinary research, integrating socio-economic and agro-ecological data.