This study examines the use of bioelectrochemical systems (BES) as an alternative to rock filters for polishing wastewater stabilisation ponds (WSPs) effluent, which often contains soluble chemical oxygen demand (SCOD) and suspended solids mainly as algal biomass. A filter type sediment BES configuration with graphite granules (as the surrogate for rocks in a rock filter) was examined. Three reactor columns were set up to examine three different treatments: (i) open-circuit without current generation; (ii) close-circuit – with current generation; and (iii) control reactor without electrode material. All columns were continuously operated for 170 days with real municipal wastewater at a hydraulic retention time of 5 days. Compared to the control reactor, the two experimental reactors showed significant improvement of SCOD removal (from approximately 25% to 66%) possibly due to retention of biomass on the graphite media. However, substantial amount of SCOD (60%) was removed via non-current generation pathways, and a very low Coulombic efficiency (6%) was recorded due to a poor cathodic oxygen reduction kinetics and a large electrode spacing. Addressing these challenges are imperative to further develop BES technology for WSP effluent treatment.