Salinization and sodification are types of degradation associated with the accumulation of salts and alkaline materials in the soil. They gradually advance unnoticed till severe degradation appears if not properly controlled. Relevant soil information is not routinely kept by many countries thus contributing to their advancement particularly in agricultural areas where their impacts have huge consequences on food security. We developed a 3‐step protocol to detect salinization and sodification advancement at different spatial scales and support soil information system development. The first step establishes an indicator database focusing on measured soil Electrical Conductivity (EC), pH, Exchangeable Sodium Percent (ESP), and a suit of environmental covariates. The second step outlines data harmonization strategies and classification of salinization and sodification problems. It also incorporates digital soil mapping for spatial information on salinization or sodification. The third step has time‐series modelling of salinization and sodification using mixed‐effects approach to improve hotspot detection in agricultural areas. The protocol was tested in Afghanistan, Sudan, and Lesotho using time‐series data between 2001 and 2018. It successfully identified salt and soda accumulation at different soil depths with more than 80% accuracy on holdout samples. In Sudan and Afghanistan, it identified topsoils as more prone to salinization than the subsoils and consequently depicted more salt accumulation in topsoils than subsoils in agricultural areas. In Lesotho, it identified emerging subsoil sodification. The protocol has potential for supporting the development of soil information on salinization and sodification which is currently lacking at many national and regional levels.