Since the mud snail Bullacta exarata was introduced for economic aquaculture in the Huanghe River (Yellow River) Delta in 2001, its quick population growth and expanded distribution make it a key-species in the intertidal zone of this area. This significantly contributed to the economic income of the local people, but its potential ecological impact on the benthic ecosystem remains unknown. A mesocosm study was conducted to test whether its bioturbation activities affect the microphytobenthos (MPBs; i.e., sedimentary microbes and unicellular algae) productivity and the nutrient exchange between the sediment-water interface. Our results show that the mud snail significantly impacted the dissolved oxygen (DO) flux across the sediment-water interface on the condition of normal sediment and light treatment, and significantly increased the ammonium efflux during recovery period in the defaunated sediment and dark treatment. The presence of micro- and meiofauna significantly increased the NH4-N flux in dark treatment. Whereas, in light treatment, these small animals had less effects on the DO and NH4-N flux between sediment-water interface. Our results provide better insight into the effect of the mud snail B. exarata on the ecosystem functioning via benthic fluxes.