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The Agro-ecological Decision Support System, MicroLEIS DSS, was applied to investigate and predict soil degradation in the province of El-Fayoum, one of the western desert areas of the Arab Republic of Egypt, with an area of 149,300 ha approximately. The Pantanal land evaluation model as one constituents of this DSS, was used for evaluating contamination risks of phosphorus, nitrogen, heavy metals and pesticides. Pantanal is an expert system model based on three kinds of input data : I) monthly meteorological data contains average values of climate variables such as mean temperature, maximum and minimum rainfall, number of days of rain and humidity, for a consecutive period of 44 years, collected from the station of El- Fayoum; II) soil survey data collected from 46 soil profiles representative of the study area and stored in the MicroLEIS SDBm plus database; and III) agricultural information on soil use and management for major crops in the area, from scientific publications of the Ministry of Agriculture. The model application results are grouped in five vulnerability classes: V1-none, V2-low, V3-moderate, V4-high and V5-Extreme for each specific contaminant. Results obtained in El-Fayoum area show that 2.8%, 45.2% and 52% of total studied area were classified as V1, V3, and V4 vulnerable land due to phosphorous contamination. On the other hand 95.9 % and 4.1% of total studied area were classified as V3, and V4 vulnerable land due to nitrogen and heavy metals, and 6.1 %, 21.5 %, 68.8 % and 2.8% of total studied area were classified as V1, V2, V3, and V4 vulnerable land due to pesticides. Additionally, Typic Torripasamment soil has a high vulnerability classes for all the types of contaminants although it represents a residual area, of 2600 ha approximately. Finally hypothetical recommended scenarios were established for each soil types in order to formulate sustainable agriculture practices by reducing inputs use like water, fertilizers and pesticides, and so minimizing the risk of soil degradation due to contamination. In conclusion, MicroLEIS DSS appears to be a useful tool in this part of arid regions, such as north of Africa (Egypt), to formulate sustaining agro-ecological systems. Although information about land resources in this part of Africa is rather scarce, these innovative agro-ecological strategies can be applied and adapted in other agricultural provinces from the Arab Republic of Egypt in order to achieve a regional sustainable land management.