The aim is to design a Simulink model which estimates the effect of rainwaters in the contaminated soil by heavy metal based on estimate the concentration of Cu, Pb, Zi, Cd, Co, Ni, Cr and Fe. So, this model would be a method to determine the contamination levels with their impact and the effect of rainwater on it. In general, mathematical models of the spread heavy metals in soil and the effect of rainwater are modeled and solved to predict the behavior of the system under different conditions. The main code that utilized and presented is MATLAB/ode45 to enable solving model equation and experience the response of the engineering systems for different applied conditions. Finally, we compare the performance of the suggested model with the traditional methods, by estimating the concentration of heavy metals before and after the rain, and then apply them in Baghdad soils after classifying it to different zones, such as: residential, industrial, commercial, agricultural and main roads. Then, compare the results of suggested methods with the results obtained by laboratory inspecting using X-Ray Fluorescence to determine the rate of accuracy.