Carbamazepine (CBZ) is a pharmaceutically active compound that has been detected in many water bodies worldwide and is classified as a micropollutant. CBZ is hardly biodegraded (removal efficiency <10%) through the conventional activated sludge process and the white-rot fungus (WRF) is reported the only microorganism to degrade it efficiently. Even though the WRF reactor has been applied to remove CBZ from wastewater, the performances varied considerably. In addition, it is still difficult to maintain a stable long-term reactor performance due to the bacterial contamination. This study aims to enhance the removal performance of WRF reactor toward CBZ under non-sterile conditions during long-term operation. The possibility of a WRF strain Phanerochaete chrysosporium immobilized on wooden chips to remove CBZ under non-sterile conditions was investigated. The CBZ removal efficiency in artificially contaminated water was improved around 30% in 7 days when the fungal immobilization was used. Adsorption was the main contributor to the CBZ removal at the early stage. However, bioremoval was considered the main removal mechanism afterwards. A countercurrent seepage bioreactor with P. chrysosporium immobilized on wooden chips was developed and continuously fed with synthetic domestic wastewater spiked with CBZ (1,000 μg/L) under non-sterile conditions for 165 days. The average removal efficiency for CBZ reached 78.28 ± 5.77%. The countercurrent seepage mode bioreactor proved to be conducive to increase the fungal resistance to the contamination by indigenous bacteria. The performance of CBZ removal was also evaluated under different reactor configuration consisted of a rotating suspension cartridge reactor immobilized with P. chrysosporium on polyurethane foam cubes. The reactor was continuously operated under non-sterile conditions for 160 days. The removal efficiency for CBZ exceeded 90% after one month of fungal adaptation by applying the intermittent operation mode and the progressive cut of external carbon source feeding. The CBZ removal mainly occurred biologically and adsorption accounted for only 7.7%. The bacterial contamination was suppressed effectively under non-sterile conditions for both reactor configurations considered as promising alternatives for the CBZ treatment in contaminated water.