Seawater intrusion significantly affects the microbial communities within coastal aquifers. Investigating the spatial distribution of groundwater microbial communities in coastal regions is crucial for understanding seawater intrusion. The primary objective of this study is to develop a novel microbial index-based method for detecting seawater intrusion. Groundwater microbial samples were collected and sent to the laboratory in the west coastal area of Longkou City, Shandong Province. By characterizing the microbial community within the whole interval of seawater intrusion into fresh groundwater and discussing the effects of salt-freshwater displacement intensities on groundwater microbial communities, including diversity, structure, and function, using indoor domestication experiments, we reveal the response of microorganisms to the seawater intrusion process under in situ environmental conditions. The results show that the microbial community diversity is highest in environments with a seawater mixing proportion (P(sm)) of 2.5% and lowest in those with a P(sm) of 75%. When considering species abundance and evolutionary processes, the microbial community structure is similar at higher P(sm) levels, while it is similar at lower P(sm) levels based on the presence or absence of species. Tenericutes, Flavobacteriia, Rhodobacterales, Flavobacteriales, Rhodobacteraceae, Flavobacteriaceae, Cohaesibacteraceae, and Cohaesibacter are significantly positively correlated with the P(sm). Strong salt-freshwater displacement enhanced the richness and evenness of the microbial community, whereas weak displacement showed the opposite trend. Strong displacement affects the functional profiles of the microbial community. This study effectively addressed the challenge of obtaining samples in coastal areas and also incorporated salt-freshwater displacement intensities, which can more comprehensively describe the microbial community characteristics within the groundwater of coastal aquifers.
