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Salination, a geochemical process related to the buildup of salts in soil and groundwater, affects the agro-ecosystems, reduces the quality of soil, limits the potential uses of groundwater, and is one of the main problems related with degradation of irrigated cropland. In the northwest region of Mexico, the Yaqui Valley is the main agricultural area with 250,000 ha of irrigated cropland. In the historical context of the ’Green Revolution’, this semiarid valley, where the ’improved variety-based agriculture’ episode originated, used to be a productive agricultural district once flourishing with grain fields, but now vast rows of wheat farmland remain unplanted since 1997, due to a drastic reduction of the water storage in the reservoir system built on the Yaqui River basin. An option that temporarily solves the water shortage in this reservoir system consists in the development of a deep-well network, by which 600 million cubic meters of groundwater can be extracted each year. Nevertheless, recent studies reported that the extracted water is classified as one with high salinity or very high salinity. A strategic approach for sustainable soil and water management became necessary to cope with this problem. The objective of this study was to investigate the spatial distribution of soil clay content and water quality extracted from wells in the Yaqui Valley’s aquifer through GIS methods. We estimated an average soil clay content of 54.52%. Salinity is considered to be one of the principal degradation risk problems in this kind of soils. The extracted water from the wells showed an average electrical conductivity (EC) of 2.1 dS m(-1). Only 7.1% of the extracted water from wells had an electrical conductivity lower than 0.7 dS m(-1) 73.4% of the cases, the EC of water extracted from wells varied from 0.7 to 3.0 dS m(-1) while in 19.5% of the wells it evidenced an EC higher than 3.0 dS m(-1). In most cases, chloride was the dominant anion, while sodium was the cation with the highest concentration. We identified the aquifer zones where water of low quality and clayey soils exist. Extracted water was found to be appropriate to irrigate moderately salt-tolerant and tolerant crops, hence, feasibility studies and following actions need to be performed to avoid irreversible degradation of the clayish soils irrigated with the available low-quality water from the aquifer. For this vast agricultural valley, salination, as one of the main factors associated with vulnerability, was defined as the degree to which human and environmental systems are likely to experience damage due to a perturbation, or to a stress caused by salinity associated to water depletion, becoming in recent years a central focus of global climatic change and arid-zone agricultural sustainability studies.