Electrodialysis is an attractive option for nutrient recovery from wastewaters like centrate, from dewatering of digested activated sludge, but cotransport of micropollutants may limit its benefit. The retention of 13 small and partly ionic micropollutants by electrodialysis was studied. All but three showed an elimination >90%. Modification of feed pH and current density were tested to improve retention. Neutral compounds like carbamazepine are retained nearly completely, independent of feed pH. Surprisingly, the retention of ionizable compounds remained unaffected by the modified feed pH despite a pK value in the investigated pH range. In synthetic feed, transport for small, ionizable compounds such as metformin or acesulfame reached up to 60% of the transport of inorganic ions. However, during treatment of centrate, cotransport of micropollutants did not exceed 30%. Moreover, in experiments at overlimiting current density, cotransport of micropollutants increased by a factor of 1.2–6 compared to underlimiting current density. This study outlines that electrodialysis effectively retains most polar organic micropollutants. However, for small, ionizable micropollutants, retention can be lower and depends on the applied current density. Increased cotransport of micropollutants should be considered when using overlimiting current densities to optimize current efficiency of nutrient recovery with electrodialysis.