Tidal wetlands undergoing regular tidal inundation contribute more than 60% CO(2) uptake of the coastal ocean. However, a comprehensive understanding of tidal microbial spatial distribution is poorly known, giving rise to previously ignored perturbations of microbial biomass in heterogeneous nearshore aquifers. In most traditional reactive models of nearshore aquifers until now, the spatio-temporal production of microbial biomass was not considered, and reaction rates depended only on the first-order decay of nutrient inputs. Here, using a biomass-based model with tidal fluctuations, we identify autotrophic and heterotrophic high biomass zones that can dictate the hot spots of aerobic respiration, nitrification, and denitrification. Crucially, the accretive microbial biomass in eutrophic environments may minimize the hydraulic conductivity and weaken the tide-driven upper saline plume, but slightly enhance seawater wedge intrusion. In addition, our simulations recreated empirical patterns of N removal in contaminated subterranean estuaries and led to a description of general rules of autotrophic and heterotrophic processes in sediments. Our findings point to previously ignored perturbations of microbial biomass to reactions in nearshore aquifers and underscore that the microbial distribution in coastal sediments has its inherent regularity to environmental alteration.