The aim of this project is to identify the relationship between cyanobacteria and invertebrates with nitrate contamination and possibility of applying these organisms as bioindicators and determining the dominant source of surface and groundwater pollution by O and N isotopes. Steady groundwater flow simulation was done using Modflow 2000 code. Water sampling locations was selected based on the results of groundwater model and local accessibility. In the first stage 23 groundwater and 7 surface water samples were collected for nitrate analysis. After analysis of first stage water samples, the mathematical model of nitrate transport in ground water was developed. Based on model results, isotopic sampling locations were determined. In the second stage, 27 groundwater and 7 surface water samples were collected for nitrate analysis. Out of these 34 water samples, 18 were chosen for analysis O and N isotopes of nitrate. O and N stable isotope analysis were carried out in the stable isotope laboratory of Cornell University in New York, USA. The results show that capture zone of the Ojeyreb drainage is about 128 Km2 within the study area. Transport model results confirm the discharge of nitrate into the drainage. Based on the results of isotopic analysis, it is inferred that the dominant source of nitrate pollution is agricultural fertilizers. However, mixing of nitrate from soil organic matter is also seen. Therefore, it is concluded that the pollution from urban and rural waste water in comparison with the agricultural waste water is negligible. According to the results of this study, 13 genus and 26 species were identified in the two stages of sampling (fall and spring 2009). L.infixa and L.mesotrichia species had negative correlation with nitrate and these species density is reduced with increase of nitrate in water. Ch.minor species show the highest positive correlation with the nitrate. So these species can be used as bioindicators of nitrate pollution. In this study, out of all Mollusca species only gastropods and bivalves were selected. There is not a specific relation between different species of Mollusca and nitrate pollution in the Ojeyreb. Therefore, they cannot be used as a bioindicatores in this area.