Quality of water changes in interaction zone between groundwater and surface water. Microorganisms that live in this interaction zone may response to changes in water quality through population density and changes in species of microorganisms. These microorganisms can therefore be used as bio-indicators and treatment of pollution. This study examined the relationship of bio-indicators with pesticide residues in groundwater and the zone of groundwater/surface water interaction. For this purpose, based on the hydrogeological investigations location of sampling points was determined. Groundwater samples were taken from the 27 wells and surface water samples were taken from 7 points in interaction zone. Syanobacterial samples were taken from that points was used for surface water sampling. Pesticide levels were measured using HPLC and Syanobacteries were identified and were counted. Based on the results Atrazine and Diazinon residues in water samples was detectable. Concentration of pesticides in groundwater is directly related to groundwater depth and recharge rate. With decreasing groundwater depth and increasing the recharge rate, residual pesticides in groundwater increases. Aph. greviellii species are most positively correlated with the pesticide concentration. O. rub and O.calcattensis species and in second order, O. chlorina and Oannae Laklr are correlated with Alachlor. These species density are increased by increasing the concentration of Atrazine. Abundance of species H. juliana and P. tenue shows a direct positive relationship with Diazinon. Adaptation and resistance of these two species shows the ability of them to use Diazinon as a source of phosphorus. Abundance of species L. mesotricha, O. subbrevis, Dermocapsa sp., O. subtilisima, P. angustissimum shows positive relation with both of Atrazine and Diazinon. Increasing the frequency of each of these specific species can be used as bio-indicator of the related pesticides.