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Sediment bioelectrochemical systems (SBESs) can be integrated into brackish aquaculture ponds for in-situ bioremediation of the pond water and sediment. Such an in-situ system offers advantages including reduced treatment cost, reusability and simple handling. In order to realize such an application potential of the SBES, in this laboratory-scale study we investigated the effect of several controllable and uncontrollable operational factors on the in-situ bioremediation performance of a tank model of a brackish aquaculture pond, into which a SBES was integrated, in comparison with a natural degradation control model. The performance was evaluated in terms of electricity generation by the SBES, Chemical oxygen demand (COD) removal and nitrogen removal of both the tank water and the tank sediment. Real-life conditions of the operational parameters were also experimented to understand the most close-to-practice responses of the system to their changes. Predictable effects of controllable parameters including external resistance and electrode spacing, similar to those reported previously for the BESs, were shown by the results but exceptions were observed. Accordingly, while increasing the electrode spacing reduced the current densities but generally improved COD and nitrogen removal, increasing the external resistance could result in decreased COD removal but also increased nitrogen removal and decreased current densities. However, maximum electricity generation and COD removal efficiency difference of the SBES (versus the control) could be reached with an external resistance of 100 Ω, not with the lowest one of 10 Ω. The effects of uncontrollable parameters such as ambient temperature, salinity and pH of the pond (tank) water were rather unpredictable. Temperatures higher than 35°C seemed to have more accelaration effect on natural degradation than on bioelectrochemical processes. Changing salinity seriously changed the electricity generation but did not clearly affect the bioremediation performance of the SBES, although at 2.5% salinity the SBES displayed a significantly more efficient removal of nitrogen in the water, compared to the control. Variation of pH to practically extreme levels (5.5 and 8.8) led to increased electricity generations but poorer performances of the SBES (vs. the control) in removing COD and nitrogen. Altogether, the results suggest some distinct responses of the SBES under brackish conditions and imply that COD removal and nitrogen removal in the system are not completely linked to bioelectrochemical processes but electrochemically enriched bacteria can still perform nonbioelectrochemical COD and nitrogen removals more efficiently than natural ones. The results confirm the application potential of the SBES in brackish aquaculture bioremediation and help propose efficient practices to warrant the success of such application in real-life scenarios.