Perfluorooctanoic acid (PFOA), even at trace levels, can cause considerable microbial responses in porous aquatic environments. We propose the use of CaCO3 to reduce PFOA migration through the formation of Ca-PFOA bonding, which impede the intracellular penetration of PFOA and thus alleviate PFOA-induced damage to microbes. In this work, a porous environment was simulated by sand columns (100 mm in height), and a thin layer of CaCO3 was placed on the top of the columns. Upon the dissolution of CaCO3, Ca2+ reduced the zeta potential of the effluent as the influent containing 2.4 μM PFOA passed through the CaCO3-containing system. This promoted the bonding of Ca-PFOA, resulting in more than a twofold increase in the blocking efficiency of PFOA during the initial 13 days. A calcite calcium armor (50–100 nm) formed on the cell surface effectively reduced the oxidative damage caused by PFOA: intracellular reactive oxygen species were reduced by 39.3 %, and bioactivity (in adenosine triphosphate) increased by 454.5 %. The alleviation of PFOA-induced stress reduced the synthesis of extracellular polymerizing substances by 67.1 %, but microbial growth remained healthy. CaCO3 introduction stimulated quorum sensing through the generation of C6-HSL to up-regulate the carbon fixation pathway. Under PFOA-induced stress, CaCO3 introduction resulted in a microbial community that was similar to that in the absence of PFOA; additionally, the dominance of denitrifying bacteria as hosts of antibiotic resistance genes (ARGs) decreased, resulting in minimal or no impact on water purification efficiency. Additionally, microbial-induced carbonate precipitation functional microorganisms were enriched as Ca2+ alleviated PFOA-induced stress. In conclusion, CaCO3 effectively alleviated PFOA-induced stress and reduced the environmental effects of PFOA on the porous aquatic environment. Microbial enhancement strategy provides a new perspective for PFOA pollution remediation.