This study is devoted to creating a neural network technology for assessing metal accumulation in the body of a metropolis resident with short-term and long-term intake from anthropogenic sources. Direct assessment of metal retention in the human body is virtually impossible due to the many internal mechanisms that ensure the kinetics of metals and the wide variety of organs, tissues, cellular structures, and secretions that ensure their functional redistribution, transport, and cumulation. We have developed an intelligent multi-neural network model capable of calculating the content of metals in the human body based on data on their environmental content. The model is two interconnected neural networks trained on actual measurement data. Since metals enter the body from the environment, the predictors of the model are metal content in drinking water and soil. In this case, water characterizes the short-term impact on the organism, and drinking water, combined with metal contents in soil, is a depository medium that accumulates metals from anthropogenic sources—the long-term impact. In addition, human physiological characteristics are taken into account in the calculations. Each period of exposure is taken into account by its neural network. Two variants of the model are proposed: open loop, where the calculation is performed by each neural network separately, and closed loop, where neural networks work together. The model built in this way was trained and tested on the data of real laboratory studies of 242 people living in different districts of Kazan. As a result, the accuracy of the neural network block for calculating long-term impact was 90% and higher, and the accuracy of the block for calculating short-term impact was 92% and higher. The closed double-loop model showed an accuracy of at least 96%. Conclusions: Our proposed method of assessing and quantifying metal accumulation in the body has high accuracy and reliability. It does not require expensive laboratory tests and allows quantifying the body’s metal accumulation content based on readily available information. The calculation results can be used as a tool for clinical diagnostics and operational and planned management to reduce the levels of polymetallic contamination in urban areas.