In this research, an exhausted ion exchange resin was used as a carrier of bacterial cells, and the resulting bio‐ion exchange resin beads were applied in batch and continuous‐flow experiments for monitoring nitrate removal. The continuous‐flow experiments investigated the effects of hydraulic retention times (HRTs) of 7–24 h on the course of denitrification; nitrate removal was achieved at HRTs longer than 9 h, with nitrate and organic removal efficiencies higher than 99 and 80%, respectively. Nitrate removal was then monitored continuously for 31 days. To investigate the influence of phosphate salts on denitrification performance, raw Cetina River water was used. The research also examined the effect of methanol addition on denitrification by decreasing the methanol‐to‐nitrogen mass ratio to 2.5:1. The obtained nitrate and organic removal efficiencies of 100 and 93%, respectively, suggest that the application of the resin beads was effective for continuous nitrate removal from surface water.