In this study, the effects of algal organic matter (AOM) from Microcystis aeruginosa on the attenuation of selected trace organic contaminants (TrOCs) were observed in managed aquifer recharge using laboratory scale soil columns. Changes in dissolved organic matter and bacteriological characteristics were also investigated to elucidate the performance of managed aquifer recharge during algal bloom. AOM exhibited a high ratio of biopolymers and low molecular weight neutrals in dissolved organic matter. Dissolved organic matter was effectively removed even after the addition of AOM (4 mg L⁻¹) in the feed water during soil passage; however, the removal rate was significantly reduced under abiotic conditions, confirming that the main removal mechanisms of dissolved organic matter involve biodegradation. AOM exhibited a much higher ratio of assimilable organic carbon/dissolved organic carbon than river water. Attenuation of four hydrophilic acid TrOCs (diclofenac, bezafibrate, ibuprofen, and ketoprofen) was significantly reduced in the presence of AOM during soil passage, but neutral TrOCs were not affected by AOM. It was difficult to remove carbamazepine using managed aquifer recharge. AOM influenced the attenuation of gemfibrozil, diclofenac, bezafibrate, ibuprofen, ketoprofen, carbamazepine, pentoxifylline, and phenacetin even after ozonation, followed by soil passage. Thus, it is important to monitor the removal of some TrOCs in managed aquifer recharge during algal blooms.