The abundant existence of antibiotics within the effluent of wastewater treatment plant seriously threatened their safety recharging. To investigate the fate and biodegradation of those toxic antibiotics within the soil aquifer system, typical antibiotics of amoxicillin (AMX) and tetracycline (TC) were selected and their removal mechanisms were investigated. Experimental results revealed that totally 93.4% and 87.2% of the AMX and TC recharged (10 μg/L) were, respectively, removed within 1 m depth column operation. Specifically, the aerobic biodegradation, abiotic processes and anoxic/anaerobic microorganism contributed as higher as 37.5%, 33.7% and 28.8% of the AMX reduction, via the controlling tests of NaN3 inhibition and soil sterilisations. By contrast, the percentage contribution of the TC was aerobic (54.3%) ˃abiotic processes (32.7%) ˃anoxic/anaerobic (13.0%), a higher aerobic degradation whereas weaker anoxic/anaerobic microorganism. Column systems (CSs) were constructed to study the effect of redox conditions (methanogenic, sulfate-reducing, nitrate-reducing, aerobic) on antibiotics degradation, and microbial community results revealed that Verrucomicrobia, Actinobacteria, Deinococcus-Thermus and Armatimonadetes contributed to the aerobic biodegradation of TC. For comparison, AMX could be efficiently degraded under nitrate reduction (19.95%) > sulfate reduction (16.64%) > methanogenic (9.53%), and Actinobacteria, Bacteroidetes and Verrucomicrobia were the dominant bacteria for AMX degradation. This study provided optimal directions for antibiotics removal within the groundwater recharging systems and is conducive to obtain highly value-added reclaimed water.