Background & Objectives: This study aimed at evaluating the water quality of thermal springs of Nir, Ardabil province, with emphasize on S. aureus bacteria, as one of the organisms that involved in skin and eye infection, in the first half of 2011. Methods: In this study, 45 samples were collected from all thermal springs of Nir from May to September. The levels of free residual chlorine, temperature, pH, turbidity, H2S, ORP, DO, and EC were measured in situ by portable devices. Total coliform, fecal coliform, Staphylococcus aurous, fecal streptococci and HPC were determined according to Standard methods for examination of water and wastewater. Results: The results showed that the highest levels of contamination to total coliform, fecal coliform, Staphylococcus aurous, and HPC were occurred in July. The lowest contamination to fecal streptococcus (maximum 11 MPN/100) was observed in August. Significant difference was observed between the months of sampling and S. aureus contamination (p<0.001). On the other hand, S. aureus contamination showed significant inverse correlation with water temperature and directly correlated with turbidity (p<0.05). There has been no statistically significant correlation between bacterial contamination and pH and H2S. Conclusion: The results showed that Staphylococcus aureus contamination level in 86.67% of samples were higher than the standard limits (MPN/100<50), which is a significant alarm for occurrence of skin diseases and probable infections to swimmers.