This study evaluates agricultural soil degradation by accumulation rates of chemical species and salinity/sodicity, their distribution, and the degree of contamination. Soil samples were collected from farmlands with intensive production system in the northern part of the Jiménez-Camargo aquifer, Chihuahua, Mexico. The physicochemical parameters and the chemical species were obtained based on Mexican regulations and UV–Vis spectrophotometry. The soil degradation was assessed using contamination-degree and soil-quality indices. A log-transformation (clr) of data facilitated cluster multivariate and related spatial distribution analysis. Chemical properties were found grouped within geogenic elements and salts. The results showed an alkaline pH with a wide range of ECe of 0.24 to 4.91 dS m−1. About 72% of the agricultural land showed a high sodicity/salinity degree, contributing to soil damage in the root zone of crops. Soil quality also is negatively affected by As, P, S, as well as salinity/sodicity, contributing to agri-environmental vulnerability of these farmlands. Hence, intensive agricultural land use contributes to severe ecological consequences such as groundwater depletion and water-quality degradation, as well as salinity/sodicity of soil, increased irrigation demand to flush salts from the soil zone, and enhancement of potentially toxic elements in soil-water-crops. In conclusion, monitoring these lands and source-water management are needed to mitigate soil-water degradation combined with agri-environmental policies through sustainability strategies that control supply and demand of land and water. The indices used here provide the metrics needed to help monitor and assess these changes for decision makers guiding sustainability and food security.