Alluvial wetlands provide an important regulating service, the water purification, through the removal of excess nutrients. In those habitats, nitrogen removal by the denitrifying bacterial community is hypothesized to interact with the co-existing invertebrate communities. Yet, few studies reported the infield relationship between invertebrate and microbial communities, where biotic and abiotic interactions are complex. We aimed at exploring the relationship between the invertebrate diversity and microbial denitrification process involved in the water purification service in an alluvial wetland. Subterranean water samplings were seasonally collected from April 2013 to March 2014. Eleven hyporheic habitats were accessed through piezometers dispersed over a meander located in the alluvial plain of the Garonne River (Southwest of France). Physicochemical, hydraulic characteristics, bacterial and invertebrate communities were simultaneously investigated as related factors for potential denitrification rates.Significant spatial gradients of invertebrate diversity, potential denitrification rates, the concentrations of dissolved oxygen, dissolved organic carbon, ammonium and nitrate ions and conductivity were observed in the groundwater of the Monbequi meander. The autumn campaign (9th October), which was performed after a long period of hydrological stability and low discharge, showed a significantly positive linear relationship between invertebrate diversity and potential denitrification rates. An overall significant and positive correlation between invertebrate and bacterial communities’ compositions was found over the four seasons. When each season was considered independently, this relationship was only significant during the autumn campaign. Such observations indicated the positive cross-communities’ interactions that existed between the invertebrate diversity—bacterial communities’ composition and their activity of denitrification. The autumn campaign was suggested to be regarded as a “hot moment” to observe this biodiversity/function relationship, when biological influences on water purification processes were probably not concealed by stronger influences of physical factors. Furthermore, this study showed that optimal potential nitrate removal was supported by a combination of biotic and abiotic conditions: relatively low temperature, oxygen and nitrate concentrations, diverse invertebrate fauna, relatively high dissolved organic carbon and ammonium concentrations.