Biogeochemical processes in groundwater-stream water mixing zone are recently of great interest because biodegradation and natural attenuation of aquatic contaminants may occur through the processes. The objectives of this study are to investigate the hydrologic and biogeochemical processes at the groundwater-stream water mixing zone through which surface water-driven nitrate may be naturally attenuated, and to examine the effect of the vertical flow exchange flux on biogeochemical processes using correlation analysis. To examine the direction of vertical water flow in the zone, vertical hydraulic gradients were measured at several depths using mini-piezometers. Microbial populations in soil samples of the zone were also analyzed by means of the polymerase chain reaction (PCR) and Cloning methods. In addition, partial correlations among vertical flow exchange, nitrate concentration and microbial activity was investigated to examine their mutual interaction. The results showed the significant interaction among the three parameters, resulting in natural attenuation of nitrate. This study showed an example of the biogeochemical fuction of groundwater-stream water mixing zone, which can be predictable from the examination of the interaction among microbial activities, concentration of contamination and vertical flow exchange flux. temperature show a significant difference in adjacent streambed, Also, the results shows that distribution of temperature was more affected by groundwater direction than intensity of flux.