Inorganic arsenic (iAs) is a carcinogen. Vegetables such as water spinach (Ipomoea aquatica Forssk.) and amaranth (Amaranthus mangostanus L.) are recognized as high-risk sources of iAs exposure because they can accumulate significant amounts of iAs and are widely consumed. To ensure safe cultivation conditions, this study aimed to establish prediction models for iAs concentration in the edible parts of water spinach and amaranth based on soil properties. Subsequently, health risk assessments associated with iAs exposure through the consumption of these vegetables were conducted using prediction models. Soil samples were collected from agricultural fields in Taiwan and used in the pot experiments. Pearson correlation and partial correlation analyses were used to explore the relationship between soil properties, including total As, clay, organic matter, iron oxides and available phosphates, and iAs concentration in edible parts of water spinach and amaranth. Prediction models based on soil properties were developed by stepwise multiple linear regression. Health risk assessments were conducted using the Monte Carlo algorithm. The results indicate that total As and organic matter contents in soil were major predictors of iAs concentration in water spinach, whereas those in amaranth were total As and clay contents. Therefore, higher health risks for consuming water spinach and amaranth are associated with higher levels of organic matter and clay contents in soil, respectively, and these are crucial factors to consider to ensure food safety. This study suggested that As-elevated soils enriched with organic matter and clay contents should be avoided when growing water spinach and amaranth, respectively.