Background and Objective: Important information can be obtained about the sources of pollutants in the atmosphere by studying the concentration of heavy metals in atmospheric precipitation.. Therefore, in this study concentrations of Pb, Zn and Cu were measured in samples of urban watershed of Bojnourd in autumn and spring seasons to help urban managers to control pollution in Bojnourd area. Materials and Methods: This study was a descriptive and cross-sectional research. 24 samples of rain water were collected to measure heavy metals. The amount of heavy metals in the samples was measured using atomic absorption. Results: Results showed that the pH was alkali in the Bojnourd urban watershed. Concentrations of Pb, Zn and Cu in rainwater in both autumn and spring were compared to international standards of WHO and EPA. The difference was significant (P <0.05) and was less than the standards values. Also, the results of the Pearson correlation test showed that the highest positive correlation was between zinc (r = 0.733) and copper (r = 0.190) in the samples of autumn and spring. This correlation was approved using hierarchical cluster analysis method. Conclusion: The low levels of pH and low concentrations of heavy metals in comparison with global standards indicated low rainwater pollution to heavy metals. Thus, there is no a health threat to the people of the city. The concentration of heavy metals in the metropolitan area of urban watersheds had been higher than other basin levels and the most dominant contaminant was lead in the residential and commercial areas with the highest urban traffic. The pollution to heavy metals varied in different seasons and the value was higher in spring rainwater samples than the autumn ones.