Electrochemical technology is promising for the selective removal of nitrate from recirculating aquaculture saltwater. For commonly used sequential batch or flowing by reactor, the electrostatic repulsion of electric double layer near cathodic surface to NO3‾ anions brings essential adsorption limit, which suppresses the efficiency of NO3‾ reduction. In order to solve this problem, an electrochemical filter was created by installing mesh electrodes with regulated thickness. During saltwater flowing through the filter, NO3‾ have to flow through cathodic holes with diameter of one and half hundred micrometers. Compared with centimeter-scale electrode gap of commonly used reactors, this micrometer-scale diffusion distance increases the concentration gradient, which intensifies NO3‾ diffusion to the cathode surface and counteracts electrostatic repulsion. In line with expectations, for 50.0 mg/L of initial nitrate-N, nitrate-N in effluent of this filter was only 2.0 mg/L, no ammonia-N and nitrite-N were detected, which met Chinese standard of water quality for aquatic mammals in aquariums (SC/T 9411-2012). While for batch process and flow-by process, the effluent concentration of nitrate-N was 60.6% and 47.6% higher than that of flow-through process, respectively. In addition, the filter displayed low energy consumption and wide availability for real recirculating aquaculture saltwater, RO wastewater and metallurgical wastewater. Furthermore, a scale-up reactor was assembled by connecting seventeen filters in series. Its water treatment capacity (5 L/h) exceeded most reported data. These results support the practicability of this novel electrochemical filter in denitrification from saltwater. Display omitted •✓ A novel electrochemical filter was built using mesh electrodes with regulated thickness.•✓ NO3‾ anion was reduced efficiently in micropores of mesh cathode.•✓ The filter achieved excellent denitrification performance compared to data in literatures.•✓ The water treatment capacity is easily scaled up by connecting filters in series.