This paper is the result of environmental geological survey engineering. Objective Seawater intrusion has become a major environmental and geological problem as well as research hotspot in coastal areas all over the world. To explore the characteristics of groundwater microbial communities in coastal areas can play a fundamental role in the management and prevention of seawater intrusion. Methods This study took two typical costal zones in Yellow Sea and Bohai Sea such as Longkou west bank and Dagu river coast. The microbial 16S rDNA of groundwater was analyzed by high–throughput sequencing method, to explore the diversity and structure characteristics of groundwater microbial communitiesin different areas. Results The groundwater in Dagu river study area was more seriously affected by seawater intrusion than that in Longkou. In Dagu river study area, the TDS concentration of groundwater was 1.06–3.19 g/L, mainly Na–Cl–HCO₃ and Na–Cl type water. In Longkou study area, the TDS of groundwater was relatively low, mainly Ca–Na–Cl–HCO₃ type water. The Alpha diversity index showed that the microbial uniformity and richness of groundwater decreased with the increasing seawater intrusion in Longkou, while the variation of microbial diversity of groundwater in Dagu river study area was complex. The groundwater microbial community structures of three monitoring wells in Longkou study area were similar, but the groundwater microbial community structures in Dagu river study area were different. The representative microorganisms of groundwater in Longkou were Burkholderiales, Comamonadaceae and Hydrogenophaga. In Dagu river study area, the representative microorganisms of groundwater are a little, only Proteobacteria was identified at the threshold St≥4.0. TOC and DO were positively correlated with bacterial abundance in groundwater in Longkou study area. In the Dagu river study area, Na⁺, Cl^–, SO₄^2– and other indicators were negatively correlated with bacterial abundance in groundwater, which was related to the long period of seawater intrusion. Conclusions This study revealed the response characteristics of groundwater microorganisms and the environment under the influence of seawater intrusion at different degrees, and showed different representative microorganisms, indicating that microbial indicators can be used as a new and effective method to identify seawater intrusion.